# HG changeset patch # User ning # Date 1363386078 14400 # Node ID cd0637465b05c8f2aa8482261b0cc52c4667963e # Parent 9cf7a632a73efd3696b42333dd3161631572fc8a Uploaded diff -r 9cf7a632a73e -r cd0637465b05 EBIsoformTwoCondTest.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/EBIsoformTwoCondTest.xml Fri Mar 15 18:21:18 2013 -0400 @@ -0,0 +1,41 @@ + + Runs EBSeq to find DE isoforms across two conditions + R --quiet --slave --file=$GALAXY_ROOT_DIR/tools/EBSeq/EBIsoformTwoCondTest.R --args $Isoform_Expression $First_Row_Sample_Names $Conditions $Ig_Vector $Target_FDR $Output $Sorted_Output $Sorted_Outpu_with_target_FDR $Sizes + + + + + + + + + + + + + + + + + + + +The input Conditions should have exactly two levels. The length of the Condition vector should be exactly the same as the number of columns in the data file (except the isoform names column). + +The Ig Vector could be generated by the GetIg function or obtained from RSEM output. + +Four output files will be generated. Each file contains Posterior probability of being DE (PPDE), Fold Change (RealFC), Posterior Fold Change (PostFC) and normalized isoform expressions. +The four files are: + +Isoforms with the same order as in input file; +Isoforms sorted by PPDE; DE Isoforms under target FDR (PPDE>=TargetFDR) +and sorted by PPDE. +Library size factor for each sample. + + + + +