'rsem-run-ebseq': Added 'output_file.condmeans' for tests with more than 2 conditions

[rsem.git] / rsem-control-fdr

diff --git a/rsem-control-fdr b/rsem-control-fdr
index 86cfb936d6e4ff91acd7f3a3c4ead43ecf6a826c..65c57cbc866277fa772ba59760d59e5c696cbfec 100755 (executable)
--- a/rsem-control-fdr
+++ b/rsem-control-fdr
@@ -74,7 +74,7 @@ rsem-control-fdr [options] input_file fdr_rate output_file
 
 =item B<input_file>
 
-This should be the result file generated by 'rsem-run-ebseq', which contains all genes/transcripts and their associated statistics.
+This should be the main result file generated by 'rsem-run-ebseq', which contains all genes/transcripts and their associated statistics.
 
 =item B<fdr_rate>
 
@@ -82,7 +82,7 @@ The desire false discovery rate (FDR).
 
 =item B<output_file>
 
-This file is a subset of the 'input_file'. It only contains the genes/transcripts called as differentially expressed (DE). When more than 2 conditions exist, DE is defined as not all conditions are equally expressed.
+This file is a subset of the 'input_file'. It only contains the genes/transcripts called as differentially expressed (DE). When more than 2 conditions exist, DE is defined as not all conditions are equally expressed.  Because statistical significance does not necessarily mean biological significance, users should also refer to the fold changes to decide which genes/transcripts are biologically significant. When more than two conditions exist, this file will not contain fold change information and users need to calculate it from 'input_file.condmeans' by themselves.
 
 =back
 
@@ -96,7 +96,7 @@ Use hard threshold method to control FDR. If this option is set, only those gene
 
 =item B<--soft-threshold>
 
-Use soft threshold method to control FDR. If this option is set, this program will try to report as many genes/transcripts as possible, as long as their average PPDE >= 1 - fdr_rate. (Default: off)
+Use soft threshold method to control FDR. If this option is set, this program will try to report as many genes/transcripts as possible, as long as their average PPDE >= 1 - fdr_rate. This option is equivalent to use EBSeq's 'crit_fun' for FDR control. (Default: off)
 
 =item B<-h/--help> 
 
@@ -114,8 +114,4 @@ We assume that we have 'GeneMat.results' as input. We want to control FDR at 0.0
 
  rsem-control-fdr GeneMat.results 0.05 GeneMat.de.txt
 
-If we instead want to use soft threshold method to obtain more called genes/transcripts, we can use:
-
- rsem-control-fdr --soft-threshold GeneMat.results 0.05 GeneMat.de.txt
-
 =cut