From 26011f2fad3bd2bb9b3b3df56c1df3778549c7e5 Mon Sep 17 00:00:00 2001 From: Bo Li <bli@cs.wisc.edu> Date: Sat, 7 Sep 2013 05:52:33 -0500 Subject: [PATCH] Fixed a displaying problem for rsem-run-ebseq's Pod document --- rsem-run-ebseq | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/rsem-run-ebseq b/rsem-run-ebseq index cd4750f..4d42491 100755 --- a/rsem-run-ebseq +++ b/rsem-run-ebseq @@ -85,8 +85,8 @@ This program is a wrapper over EBSeq. It performs differential expression analys This file reports the calculated statistics for all genes/transcripts. It is written as a matrix with row and column names. The row names are the genes'/transcripts' names. The column names are for the reported statistics. -If there are only 2 different conditions among the samples, four statistics (columns) will be reported for each gene/transcript. They are "PPEE", "PPDE", "PostFC" and "RealFC". "PPEE" is the posterior probability (estimated by EBSeq) that a gene/transcript is equally expressed. "PPDE" is the posterior probability that a gene/transcript is differentially expressed. "PostFC" is the posterior fold change (condition 1 over condition2) for a gene/transcript. It is defined as the ratio between posterior mean expression estimates of the gene/transcript for each condition. "RealFC" is the real fold change (condition 1 over condition2) for a gene/transcript. It is the ratio of the normalized within condition 1 mean count over normalized within condition 2 mean count for the gene/transcript. Fold changes are calculated using EBSeq's 'PostFC' function. The genes/transcripts are reported in descending order of their "PPDE" values. - +If there are only 2 different conditions among the samples, four statistics (columns) will be reported for each gene/transcript. They are "PPEE", "PPDE", "PostFC" and "RealFC". "PPEE" is the posterior probability (estimated by EBSeq) that a gene/transcript is equally expressed. "PPDE" is the posterior probability that a gene/transcript is differentially expressed. "PostFC" is the posterior fold change (condition 1 over condition2) for a gene/transcript. It is defined as the ratio between posterior mean expression estimates of the gene/transcript for each condition. "RealFC" is the real fold change (condition 1 over condition2) for a gene/transcript. It is the ratio of the normalized within condition 1 mean count over normalized within condition 2 mean count for the gene/transcript. Fold changes are calculated using EBSeq's 'PostFC' function. The genes/transcripts are reported in descending order of their "PPDE" values. + If there are more than 2 different conditions among the samples, the output format is different. For differential expression analysis with more than 2 conditions, EBSeq will enumerate all possible expression patterns (on which conditions are equally expressed and which conditions are not). Suppose there are k different patterns, the first k columns of the output file give the posterior probability of each expression pattern is true. Patterns are defined in a separate file, 'output_file.pattern'. The k+1 column gives the maximum a posteriori (MAP) expression pattern for each gene/transcript. The k+2 column gives the posterior probability that not all conditions are equally expressed (column name "PPDE"). The genes/transcripts are reported in descending order of their "PPDE" column values. For details on how EBSeq works for more than 2 conditions, please refer to EBSeq's manual. =item B<output_file.pattern> -- 2.39.5