Mercurial > repos > genouest > askor_de

diff AskoR_DE.R @ 2:f7dde9cca31e draft default tip

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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/askor commit 994ecff7807bb0eb9dac740d67ad822415b0b464
author genouest
date Thu, 19 Apr 2018 03:44:16 -0400
parents d24096d4c002
children
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--- a/AskoR_DE.R	Wed Apr 18 06:25:35 2018 -0400
+++ b/AskoR_DE.R	Thu Apr 19 03:44:16 2018 -0400
@@ -2,7 +2,7 @@
 source(paste0(askor_path,"/AskoR.R"))
 
 ##############################################
-##                Parameters                ##
+##                Parameters                ##  
 ##############################################
 
 parameters<-Asko_start()
@@ -31,7 +31,7 @@
 cat("Total number of genes : ", dim(data$dge$counts)[1], "\n")
 cat("Total number of samples : ", dim(data$dge$counts)[2], "\n")
 cat("summary of CPM by samples\n")
-summary(cpm(data$dge))
+summary(cpm(data$dge, normalized.lib.sizes=FALSE))
 pdf(parameters$output_pdf)
 asko_data<-asko3c(data)
 cat("Filtering genes with more than ", parameters$threshold_cpm, " CPM in ",parameters$replicate_cpm,"samples\n")
@@ -42,3 +42,5 @@
 cat("Statistical analysis\n")
 DEanalysis(asko_norm,data, asko_data,parameters)
 dev.off()
+
+