argument "intgroup" is missing in arrayQualityMetrics
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@13117882295-10179
Last seen 8.6 years ago

 

> source("http://bioconductor.org/biocLite.R")

> biocLite("ArrayExpress")

> library("ArrayExpress")

> getwd()

> setwd("D:/test")

> AEset<-ArrayExpress("E-GEOD-470")

> save(AEset, file="AEset.RData")

>load("AEset.rdata")

> class(AEset)

> AEset

> pData(AEset)

> colnames(pData(AEset))

>fac<colnames(pData(AEset))[grep("Factor",colnames(pData(AEset)))] ;

 >fac

  [1] "Factor.Value..DiseaseState."        "Factor.Value..EnvironmentalStress." "Factor.Value..Time."

> library(arrayQualityMetrics)

> arrayQualityMetrics(expressionset=AEset, outdir="QAraw",force=FALSE, do.logtransform=TRUE, intgroup=fac)

The report will be written into directory 'QAraw'. 
Error in match(x, table, nomatch = 0L) : 
  argument "intgroup" is missing, with no default
 
Idon’t know what’s the problem in my steps? And how can i fix it?

 

arrayQualityMetrics • 1.4k views
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