diff ImportDataFromMatrix.R @ 37:25b828010ca9 draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit bfd179bd7fb4796e21183e0e4de2fcf78ca35b7d

--- a/ImportDataFromMatrix.R	Fri Jun 22 04:30:31 2018 -0400
+++ b/ImportDataFromMatrix.R	Mon Jun 25 04:11:22 2018 -0400
@@ -66,13 +66,10 @@
 colnames(conditions)=c("source_name_ch1","description")
 phenodata<-new("AnnotatedDataFrame",data=conditions)
 
-head(data)
-conditions
-
 eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation)
 
 if (normalization == "quantile") {
-	eset <- normalize.ExpressionSet.quantiles(eset, transfn="log2")
+	eset <- normalize.ExpressionSet.quantiles(eset, transfn="log")
 } else if (normalization == "log2") {
 	exprs(eset) = log2(exprs(eset)) 
 }