SOCR EduMaterials AnalysesCommandLineFDR Correction - Revision history

Dinov: /* Supplementary information */

2016-02-03T14:35:55Z

‎Supplementary information

IvoDinov at 05:31, 26 April 2012

2012-04-26T05:31:46Z

IvoDinov at 22:01, 18 October 2011

2011-10-18T22:01:19Z

IvoDinov: /* Validation */ added Pipeline image

2011-06-09T22:17:42Z

‎Validation: added Pipeline image

IvoDinov: /* Validation */

2011-06-09T22:00:34Z

‎Validation

IvoDinov: /* Validation */

2011-06-09T22:00:03Z

‎Validation

IvoDinov: /* Validation */

2011-06-09T21:58:27Z

‎Validation

IvoDinov at 21:51, 9 June 2011

2011-06-09T21:51:44Z

IvoDinov: /* FDR Usage */ added a description of the p-value thresholding and masking protocol

2011-06-08T18:22:38Z

‎FDR Usage: added a description of the p-value thresholding and masking protocol

IvoDinov at 01:54, 21 July 2009

2009-07-21T01:54:10Z

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 ===Supplementary information===
 * [http://en.wikipedia.org/wiki/False_discovery_rate False Discovery Rate (FDR)]
 * [http://lib.stat.cmu.edu/~genovese/talks/hannover1-04.pdf FDR Tutorial]

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 *** ''other'' = default processor (java.nio.ByteOrder.nativeOrder())
 ** -verbose: to report all input and corrected-output p-values (avoid!)
 ====Shape-based p-Value FDR correction example====

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 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>.
-The [[SOCR]] analysis implementation of FDR is based on [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/12/2921 this article].
+The [[SOCR]] analysis implementation of FDR is based on [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/12/2921 this article], see [[SOCR_EduMaterials_AnalysesCommandLineFDR_Correction#References|references below]].
 ===FDR Usage===
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 * [http://lib.stat.cmu.edu/~genovese/talks/hannover1-04.pdf FDR Tutorial]
 * [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/12/2921 FDR/R implementation]
 {{translate|pageName=http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFDR_Correction}}

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 ===Validation===
 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:
 * Input Files:

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 * Explicit validation scripts:
 : Calculation of FDR corrected p-values without masking (output: FDR_q0.05_Raw_P.txt):
-:: <code>java -ms500m -mx1000m -cp /usr/local/loniJars/SOCR_Statistics/SOCR_core.j
+:: <code>java -ms500m -mx1000m -cp /usr/local/loniJars/SOCR_Statistics/SOCR_core.jar:/usr/local/loniJars/SOCR_Statistics/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.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>
 : Calculation of FDR corrected p-values using the (manually) pre-masked p-values (output: FDR_NoMask_PreMaskedRaw_P.txt):
-:: <code>java -ms500m -mx1000m -cp /usr/local/loniJars/SOCR_Statistics/SOCR_core.j
+:: <code>java -ms500m -mx1000m -cp /usr/local/loniJars/SOCR_Statistics/SOCR_core.jar:/usr/local/loniJars/SOCR_Statistics/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.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>
 : Calculation of FDR corrected p-values by providing the mask file to the FDR-calculator (output: FDR_UsingMask_Raw_P_values.txt):
-:: <code>java -ms500m -mx1000m -cp /usr/local/loniJars/SOCR_Statistics/SOCR_core.j
+:: <code>java -ms500m -mx1000m -cp /usr/local/loniJars/SOCR_Statistics/SOCR_core.jar:/usr/local/loniJars/SOCR_Statistics/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.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>
 ===Supplementary information===

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 |}
 </center>
 ===Supplementary information===

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 *** 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.
 *** ''Dependence'': If this option is included, it must be preceded by "-type".
 ** -fdr_rate [double]: the False Discovery Rate level (e.g., 0.05)
 ** -number [int]: enter the number of P-values stored in the input file (output file will have the same number of floats).