http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFDR_Correction&feed=atom&action=history
SOCR EduMaterials AnalysesCommandLineFDR Correction - Revision history
2024-03-28T19:28:47Z
Revision history for this page on the wiki
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http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFDR_Correction&diff=12471&oldid=prev
IvoDinov at 14:33, 3 February 2016
2016-02-03T14:33:54Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Supplementary information===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Supplementary information===</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* [http://wiki.socr.umich.edu/index.php/SMHS_CorrectionMultipleTesting#FDR_.28false_discovery_rate.29 FDR Correction protocol, SMHS EBook]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://en.wikipedia.org/wiki/False_discovery_rate False Discovery Rate (FDR)]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://en.wikipedia.org/wiki/False_discovery_rate False Discovery Rate (FDR)]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://lib.stat.cmu.edu/~genovese/talks/hannover1-04.pdf FDR Tutorial]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://lib.stat.cmu.edu/~genovese/talks/hannover1-04.pdf FDR Tutorial]</div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFDR_Correction&diff=11613&oldid=prev
IvoDinov at 05:31, 26 April 2012
2012-04-26T05:31:46Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*** ''other'' = default processor (java.nio.ByteOrder.nativeOrder())</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*** ''other'' = default processor (java.nio.ByteOrder.nativeOrder())</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -verbose: to report all input and corrected-output p-values (avoid!)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -verbose: to report all input and corrected-output p-values (avoid!)</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">===Try-It-Online===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">You can test the FDR functionality using the [http://ucla.in/Ie80ps Pipeline PWS Web-start server].</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Shape-based p-Value FDR correction example====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Shape-based p-Value FDR correction example====</div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFDR_Correction&diff=11348&oldid=prev
IvoDinov at 22:01, 18 October 2011
2011-10-18T22:01:19Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Then, FDR guarantees that the [[AP_Statistics_Curriculum_2007_Distrib_MeanVar |expectation]] of the relative-false-discovery (falsely-rejecting Ho, when it's true) is <math>E \left ( {FD \over D}\right ) \leq \alpha</math>.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Then, FDR guarantees that the [[AP_Statistics_Curriculum_2007_Distrib_MeanVar |expectation]] of the relative-false-discovery (falsely-rejecting Ho, when it's true) is <math>E \left ( {FD \over D}\right ) \leq \alpha</math>.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The [[SOCR]] analysis implementation of FDR is based on [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/12/2921 this article].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The [[SOCR]] analysis implementation of FDR is based on [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/12/2921 this article<ins class="diffchange diffchange-inline">], see [[SOCR_EduMaterials_AnalysesCommandLineFDR_Correction#References|references below]</ins>].</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===FDR Usage===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===FDR Usage===</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://lib.stat.cmu.edu/~genovese/talks/hannover1-04.pdf FDR Tutorial]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://lib.stat.cmu.edu/~genovese/talks/hannover1-04.pdf FDR Tutorial]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/12/2921 FDR/R implementation]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/12/2921 FDR/R implementation]</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">===References===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* Che, Annie, Cui, Jenny, and Dinov, Ivo (2009). [http://www.jstatsoft.org/v30/i03 SOCR Analyses: Implementation and Demonstration of a New Graphical Statistics Educational Toolkit]. JSS, Vol. 30, Issue 3, Apr 2009.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* Scheid, S and Spang, R. (2005) Gene expression: twilight; a Bioconductor package for estimating the local false discovery rate. Bioinformatics 21(12): 2921-2922, [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/12/2921 doi:10.1093/bioinformatics/bti436]</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* Che, A, Cui, J, and Dinov, ID (2009) [http://jolt.merlot.org/vol5no1/dinov_0309.htm SOCR Analyses – an Instructional Java Web-based Statistical Analysis Toolkit], JOLT, 5(1), 1-19, March 2009.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* Dinov, ID. [http://www.jstatsoft.org/v16/i11 Statistics Online Computational Resource], Journal of Statistical Software, Vol. 16, No. 1, 1-16, October 2006. </ins></div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFDR_Correction&diff=11048&oldid=prev
IvoDinov: /* Validation */ added Pipeline image
2011-06-09T22:17:42Z
<p><span class="autocomment">Validation: </span> added Pipeline image</p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Validation===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Validation===</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Image:SOCR_EduMaterials_AnalysesCommandLineFDR_Correction_Fig3.png|300px|thumbnail|right| Pipeline FDR Validation Protocol.]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The SOCR FDR calculator was validated using the following protocol. The following [http://wiki.stat.ucla.edu/socr/uploads/9/99/FDR_Validation_June_2011.zip ZIP archive] contains data, validation protocol and a [http://pipeline.loni.ucla.edu pipeline graphical workflow] implementation of this validation protocol. This protocol uses the following data:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The SOCR FDR calculator was validated using the following protocol. The following [http://wiki.stat.ucla.edu/socr/uploads/9/99/FDR_Validation_June_2011.zip ZIP archive] contains data, validation protocol and a [http://pipeline.loni.ucla.edu pipeline graphical workflow] implementation of this validation protocol. This protocol uses the following data:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Input Files:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Input Files:</div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFDR_Correction&diff=11046&oldid=prev
IvoDinov: /* Validation */
2011-06-09T22:00:34Z
<p><span class="autocomment">Validation</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Explicit validation scripts:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Explicit validation scripts:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values without masking (output: FDR_q0.05_Raw_P.txt):</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values without masking (output: FDR_q0.05_Raw_P.txt):</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: <code>java -ms500m -mx1000m -cp /usr/local/loniJars/SOCR_Statistics/SOCR_core.<del class="diffchange diffchange-inline">j</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: <code>java -ms500m -mx1000m -cp /usr/local/loniJars/SOCR_Statistics/SOCR_core.<ins class="diffchange diffchange-inline">jar</ins>:/usr/local/loniJars/SOCR_Statistics/SOCR_plugin.jar edu.ucla.stat.SOCR.<ins class="diffchange diffchange-inline">analyses</ins>.command.volume.Test_FDR -input Raw_P.txt -output FDR_q0.05_Raw_P.txt -type 0 -fdr_rate 0.05 -number 100 -byteorder little</code></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">ar</del>:/usr/local/loniJars/SOCR_Statistics/SOCR_plugin.jar edu.ucla.stat.SOCR.<del class="diffchange diffchange-inline">analys</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">es</del>.command.volume.Test_FDR -input Raw_P.txt -output FDR_q0.05_Raw_P.txt -type 0 -fdr_rate 0.05 -number 100 -byteorder little</code></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values using the (manually) pre-masked p-values (output: FDR_NoMask_PreMaskedRaw_P.txt):</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values using the (manually) pre-masked p-values (output: FDR_NoMask_PreMaskedRaw_P.txt):</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: <code>java -ms500m -mx1000m -cp /usr/local/loniJars/SOCR_Statistics/SOCR_core.<del class="diffchange diffchange-inline">j</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: <code>java -ms500m -mx1000m -cp /usr/local/loniJars/SOCR_Statistics/SOCR_core.<ins class="diffchange diffchange-inline">jar</ins>:/usr/local/loniJars/SOCR_Statistics/SOCR_plugin.jar edu.ucla.stat.SOCR.<ins class="diffchange diffchange-inline">analyses</ins>.command.volume.Test_FDR -input PreMasked_41_P.txt -output FDR_NoMask_PreMaskedRaw_P.txt -type 0 -fdr_rate 0.05 -number 52 -byteorder little</code></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">ar</del>:/usr/local/loniJars/SOCR_Statistics/SOCR_plugin.jar edu.ucla.stat.SOCR.<del class="diffchange diffchange-inline">analys</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">es</del>.command.volume.Test_FDR -input PreMasked_41_P.txt -output FDR_NoMask_PreMaskedRaw_P.txt -type 0 -fdr_rate 0.05 -number 52 -byteorder little</code></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values by providing the mask file to the FDR-calculator (output: FDR_UsingMask_Raw_P_values.txt):</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values by providing the mask file to the FDR-calculator (output: FDR_UsingMask_Raw_P_values.txt):</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: <code>java -ms500m -mx1000m -cp /usr/local/loniJars/SOCR_Statistics/SOCR_core.<del class="diffchange diffchange-inline">j</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: <code>java -ms500m -mx1000m -cp /usr/local/loniJars/SOCR_Statistics/SOCR_core.<ins class="diffchange diffchange-inline">jar</ins>:/usr/local/loniJars/SOCR_Statistics/SOCR_plugin.jar edu.ucla.stat.SOCR.<ins class="diffchange diffchange-inline">analyses</ins>.command.volume.Test_FDR -input Raw_P.txt -output FDR_UsingMask_Raw_P_values.txt -type 0 -fdr_rate 0.05 -number 100 -byteorder little -mask Mask.txt</code></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">ar</del>:/usr/local/loniJars/SOCR_Statistics/SOCR_plugin.jar edu.ucla.stat.SOCR.<del class="diffchange diffchange-inline">analys</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">es</del>.command.volume.Test_FDR -input Raw_P.txt -output FDR_UsingMask_Raw_P_values.txt -type 0 -fdr_rate 0.05 -number 100 -byteorder little -mask Mask.txt</code></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Supplementary information===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Supplementary information===</div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFDR_Correction&diff=11045&oldid=prev
IvoDinov: /* Validation */
2011-06-09T22:00:03Z
<p><span class="autocomment">Validation</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Explicit validation scripts:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Explicit validation scripts:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values without masking (output: FDR_q0.05_Raw_P.txt):</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values without masking (output: FDR_q0.05_Raw_P.txt):</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: <code>/usr/local/<del class="diffchange diffchange-inline">loniScripts</del>/<del class="diffchange diffchange-inline">loniStats</del>/<del class="diffchange diffchange-inline">FDR_Correction_Text</del>.<del class="diffchange diffchange-inline">sh </del>-input Raw_P.txt -output FDR_q0.05_Raw_P.txt -type 0 -fdr_rate 0.05 -number 100 -byteorder little</code></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: <code><ins class="diffchange diffchange-inline">java -ms500m -mx1000m -cp </ins>/usr/local/<ins class="diffchange diffchange-inline">loniJars</ins>/<ins class="diffchange diffchange-inline">SOCR_Statistics</ins>/<ins class="diffchange diffchange-inline">SOCR_core</ins>.<ins class="diffchange diffchange-inline">j</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">ar:/usr/local/loniJars/SOCR_Statistics/SOCR_plugin.jar edu.ucla.stat.SOCR.analys</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">es.command.volume.Test_FDR </ins>-input Raw_P.txt -output FDR_q0.05_Raw_P.txt -type 0 -fdr_rate 0.05 -number 100 -byteorder little</code></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values using the (manually) pre-masked p-values (output: FDR_NoMask_PreMaskedRaw_P.txt):</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values using the (manually) pre-masked p-values (output: FDR_NoMask_PreMaskedRaw_P.txt):</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: <code>/usr/local/<del class="diffchange diffchange-inline">loniScripts</del>/<del class="diffchange diffchange-inline">loniStats</del>/<del class="diffchange diffchange-inline">FDR_Correction_Text</del>.<del class="diffchange diffchange-inline">sh </del>-input PreMasked_41_P.txt -output FDR_NoMask_PreMaskedRaw_P.txt -type 0 -fdr_rate 0.05 -number 52 -byteorder little</code></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: <code><ins class="diffchange diffchange-inline">java -ms500m -mx1000m -cp </ins>/usr/local/<ins class="diffchange diffchange-inline">loniJars</ins>/<ins class="diffchange diffchange-inline">SOCR_Statistics</ins>/<ins class="diffchange diffchange-inline">SOCR_core</ins>.<ins class="diffchange diffchange-inline">j</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">ar:/usr/local/loniJars/SOCR_Statistics/SOCR_plugin.jar edu.ucla.stat.SOCR.analys</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">es.command.volume.Test_FDR </ins>-input PreMasked_41_P.txt -output FDR_NoMask_PreMaskedRaw_P.txt -type 0 -fdr_rate 0.05 -number 52 -byteorder little</code></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values by providing the mask file to the FDR-calculator (output: FDR_UsingMask_Raw_P_values.txt):</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values by providing the mask file to the FDR-calculator (output: FDR_UsingMask_Raw_P_values.txt):</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: <code>/usr/local/<del class="diffchange diffchange-inline">loniScripts</del>/<del class="diffchange diffchange-inline">loniStats</del>/<del class="diffchange diffchange-inline">FDR_Correction_Text</del>.<del class="diffchange diffchange-inline">sh </del>-input Raw_P.txt -output FDR_UsingMask_Raw_P_values.txt -type 0 -fdr_rate 0.05 -number 100 -byteorder little -mask Mask.txt</code></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: <code><ins class="diffchange diffchange-inline">java -ms500m -mx1000m -cp </ins>/usr/local/<ins class="diffchange diffchange-inline">loniJars</ins>/<ins class="diffchange diffchange-inline">SOCR_Statistics</ins>/<ins class="diffchange diffchange-inline">SOCR_core</ins>.<ins class="diffchange diffchange-inline">j</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">ar:/usr/local/loniJars/SOCR_Statistics/SOCR_plugin.jar edu.ucla.stat.SOCR.analys</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">es.command.volume.Test_FDR </ins>-input Raw_P.txt -output FDR_UsingMask_Raw_P_values.txt -type 0 -fdr_rate 0.05 -number 100 -byteorder little -mask Mask.txt</code></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Supplementary information===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Supplementary information===</div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFDR_Correction&diff=11044&oldid=prev
IvoDinov: /* Validation */
2011-06-09T21:58:27Z
<p><span class="autocomment">Validation</span></p>
<table style="background-color: white; color:black;">
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 21:58, 9 June 2011</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Validation===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Validation===</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The SOCR FDR calculator was validated using the following protocol. The following [ ZIP archive] contains data, validation protocol and a [http://pipeline.loni.ucla.edu pipeline graphical workflow] implementation of this validation protocol. This protocol uses the following data:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The SOCR FDR calculator was validated using the following protocol. The following [<ins class="diffchange diffchange-inline">http://wiki.stat.ucla.edu/socr/uploads/9/99/FDR_Validation_June_2011.zip </ins>ZIP archive] contains data, validation protocol and a [http://pipeline.loni.ucla.edu pipeline graphical workflow] implementation of this validation protocol. This protocol uses the following data:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Input Files:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Input Files:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Raw_P.txt - 100 random numbers in (0,1)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Raw_P.txt - 100 random numbers in (0,1)</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 2,114:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values by providing the mask file to the FDR-calculator (output: FDR_UsingMask_Raw_P_values.txt):</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: Calculation of FDR corrected p-values by providing the mask file to the FDR-calculator (output: FDR_UsingMask_Raw_P_values.txt):</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:: <code>/usr/local/loniScripts/loniStats/FDR_Correction_Text.sh -input Raw_P.txt -output FDR_UsingMask_Raw_P_values.txt -type 0 -fdr_rate 0.05 -number 100 -byteorder little -mask Mask.txt</code></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>:: <code>/usr/local/loniScripts/loniStats/FDR_Correction_Text.sh -input Raw_P.txt -output FDR_UsingMask_Raw_P_values.txt -type 0 -fdr_rate 0.05 -number 100 -byteorder little -mask Mask.txt</code></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Supplementary information===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Supplementary information===</div></td></tr>
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</table>
IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFDR_Correction&diff=11042&oldid=prev
IvoDinov at 21:51, 9 June 2011
2011-06-09T21:51:44Z
<p></p>
<table style="background-color: white; color:black;">
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<td colspan='2' style="background-color: white; color:black;">Revision as of 21:51, 9 June 2011</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></center></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></center></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">===Validation===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The SOCR FDR calculator was validated using the following protocol. The following [ ZIP archive] contains data, validation protocol and a [http://pipeline.loni.ucla.edu pipeline graphical workflow] implementation of this validation protocol. This protocol uses the following data:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* Input Files:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">: Raw_P.txt - 100 random numbers in (0,1)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">: Mask.txt - mask file (1=inside, 0=outside)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">: PreMasked_41_P.txt - applying the mask to the raw p-values (premasked_pvalue - raw_pvalue * mask)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* The protocol generates the following output FDR corrected p-value results:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">: FDR_NoMask_PreMaskedRaw_P.txt</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">: FDR_q0.05_Raw_P.txt</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">: FDR_UsingMask_Raw_P_values.txt</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* Explicit validation scripts:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">: Calculation of FDR corrected p-values without masking (output: FDR_q0.05_Raw_P.txt):</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">:: <code>/usr/local/loniScripts/loniStats/FDR_Correction_Text.sh -input Raw_P.txt -output FDR_q0.05_Raw_P.txt -type 0 -fdr_rate 0.05 -number 100 -byteorder little</code></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">: Calculation of FDR corrected p-values using the (manually) pre-masked p-values (output: FDR_NoMask_PreMaskedRaw_P.txt):</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">:: <code>/usr/local/loniScripts/loniStats/FDR_Correction_Text.sh -input PreMasked_41_P.txt -output FDR_NoMask_PreMaskedRaw_P.txt -type 0 -fdr_rate 0.05 -number 52 -byteorder little</code></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">: Calculation of FDR corrected p-values by providing the mask file to the FDR-calculator (output: FDR_UsingMask_Raw_P_values.txt):</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">:: <code>/usr/local/loniScripts/loniStats/FDR_Correction_Text.sh -input Raw_P.txt -output FDR_UsingMask_Raw_P_values.txt -type 0 -fdr_rate 0.05 -number 100 -byteorder little -mask Mask.txt</code></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Supplementary information===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Supplementary information===</div></td></tr>
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</table>
IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFDR_Correction&diff=11041&oldid=prev
IvoDinov: /* FDR Usage */ added a description of the p-value thresholding and masking protocol
2011-06-08T18:22:38Z
<p><span class="autocomment">FDR Usage: </span> added a description of the p-value thresholding and masking protocol</p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 18:22, 8 June 2011</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*** Masks for raw binary volumes must be binary 1-byte volumes of the exact same dimensions as the input volume of raw 4-byte floating p-values.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*** Masks for raw binary volumes must be binary 1-byte volumes of the exact same dimensions as the input volume of raw 4-byte floating p-values.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*** ''Dependence'': If this option is included, it must be preceded by "-type".</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*** ''Dependence'': If this option is included, it must be preceded by "-type".</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">*** ''Caution'': Be careful with using masks to FDR correct p-values. P-values outside of the mask are ignored. The skeleton of the Masking and FDR-correction code is as follows:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">::: <code>if (mask_volume.readUnsignedByte()>0) maskVolumeBoolean[i]=true; // get mask</code></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">::: <code>if (maskVolumeBoolean[i]) maskedPValues[counter] = p_values[i]; // mask raw_p_values</code></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">::: <code>thresholdedPMap = FDR(maskedPValues, fdr_rate).getThresholdedArray(); // FDR threshold masked p_values</code></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">::: <code>if (maskVolumeBoolean[i]) FDR_corrected_PValues[i] = thresholdedPMap[counter]; // Save thresholded p_values</code></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">::: <code>else FDR_corrected_PValues[i] = 1.0;</code></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -fdr_rate [double]: the False Discovery Rate level (e.g., 0.05)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -fdr_rate [double]: the False Discovery Rate level (e.g., 0.05)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -number [int]: enter the number of P-values stored in the input file (output file will have the same number of floats).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -number [int]: enter the number of P-values stored in the input file (output file will have the same number of floats).</div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFDR_Correction&diff=9236&oldid=prev
IvoDinov at 01:54, 21 July 2009
2009-07-21T01:54:10Z
<p></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 01:54, 21 July 2009</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*** ''little'' = LITTLE_ENDIAN processor</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*** ''little'' = LITTLE_ENDIAN processor</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*** ''other'' = default processor (java.nio.ByteOrder.nativeOrder())</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*** ''other'' = default processor (java.nio.ByteOrder.nativeOrder())</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">** -verbose: to report all input and corrected-output p-values (avoid!)</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Shape-based p-Value FDR correction example====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>====Shape-based p-Value FDR correction example====</div></td></tr>
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