[BioC] nsFilter give error saying \"invalid subscripts type \'list\'\"
Hao [guest]
guest at bioconductor.org
Wed Mar 20 20:38:57 CET 2013
Dear All:
I tried to use nsFilter but keeps getting this error:
Error in rows[i] : invalid subscript type 'list'
I do not know what went wrong, please help...
-- output of sessionInfo():
my code:
exprs <- read.table("cia-filtered-dataframe.txt", header=TRUE, sep="\t", row.names=1, as.is=TRUE)
exprx<-as.matrix(exprs)
pData <- read.table("cia-phenodata.txt",row.names=1, header=T,sep="\t", as.is=TRUE)
phenoData <- new("AnnotatedDataFrame",data=pData)
annotation <- "mouse4302.db"
cia <- ExpressionSet(assayData=exprx,phenoData=phenoData,annotation="mouse4302.db")
library(genefilter)
filtered_eset <- nsFilter(cia, require.entrez=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.filter=FALSE, var.cutoff=0.25, filterByQuantile=TRUE, feature.exclude="^AFFX")
--
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