Mercurial > repos > sblanck > smagexp

comparison ImportDataFromMatrix.R @ 37:25b828010ca9 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit bfd179bd7fb4796e21183e0e4de2fcf78ca35b7d
author sblanck
date Mon, 25 Jun 2018 04:11:22 -0400
parents 7f74250a083d
children c08b824e40cc
comparison
equal deleted inserted replaced
36:22e1325aaa88 37:25b828010ca9
64 htmlfile=readChar(result.template, file.info(result.template)$size) 64 htmlfile=readChar(result.template, file.info(result.template)$size)
65 65
66 colnames(conditions)=c("source_name_ch1","description") 66 colnames(conditions)=c("source_name_ch1","description")
67 phenodata<-new("AnnotatedDataFrame",data=conditions) 67 phenodata<-new("AnnotatedDataFrame",data=conditions)
68 68
69 head(data)
70 conditions
71
72 eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation) 69 eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation)
73 70
74 if (normalization == "quantile") { 71 if (normalization == "quantile") {
75 eset <- normalize.ExpressionSet.quantiles(eset, transfn="log2") 72 eset <- normalize.ExpressionSet.quantiles(eset, transfn="log")
76 } else if (normalization == "log2") { 73 } else if (normalization == "log2") {
77 exprs(eset) = log2(exprs(eset)) 74 exprs(eset) = log2(exprs(eset))
78 } 75 }
79 76
80 boxplotnorm="boxplotnorm.png" 77 boxplotnorm="boxplotnorm.png"