=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>
=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
=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>
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