[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)

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")

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")

Sent via the guest posting facility at bioconductor.org.

More information about the Bioconductor mailing list