Error in the package of "genefilter" "nsFilter"
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Lian Liu ▴ 20
@lian-liu-11570
Last seen 6.9 years ago
Tokyo

Dear all,

I am so sorry that I'm almost reposting my question. I performed normalization of an HTA 2.0 array and I wanted to perform non-specific genefiltering. But I met an error which I don't know how to deal with.

My codes are:

>library(pd.hta.2.0)

>library(oligo)

>GSE12345cels = list.celfiles()

>GSE12345raw = read.celfiles(GSE12345cels)

>GSE12345.rma = rma(GSE12345raw, target='core')

>GSE12345exp<-exprs(GSE12345.rma)

 

>library(affycoretools)

>GSE12345.rma<-annotateEset(GSE12345.rma,pd.hta.2.0,type = "core")

 

>GSE12345pData=read.csv("/Users/lian/Documents/GSE12345/GSE12345pData.csv",row.names=1, header=T)

>metadata <- data.frame(labelDescription=c("Disease state","Tissue origin"),rownames=c("AFSR","Tissue"))

>GSE12345phenoData <- new("AnnotatedDataFrame",data= GSE12345pData, varMetadata=metadata)

 

>GSE12345annotation <- "pd.hta.2.0"

 

>GSE12345expressionSet <- ExpressionSet(assayData= GSE12345exp,phenoData= GSE12345phenoData, annotation= GSE12345annotation)

 

>library(genefilter)

>GSE12345f <- nsFilter(GSE12345expressionSet)

 

And here is the error:

Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘columns’ for signature ‘"AffyHTAPDInfo"’

Could anyone please give me some suggestions?

Thank you very much.

 

genefilter • 1.2k views
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@james-w-macdonald-5106
Last seen 8 hours ago
United States

The annotation slot for an ExpressionSet is supposed to contain the name of a package that can be used to map probeset IDs to information about the genes/transcripts the probesets are intended to measure. For this array that would be the hta20transcriptcluster.db package (for the current release I incorrectly called this package the hta20sttranscriptcluster.db package - note the extra bolded ST in that name - so you need to use the correct package name, dependent on the version of BioC you are using).

The pd.hta.2.0 package is used to map probes to probesets when you are summarizing the data, and isn't the kind of package that nsFilter is looking for.
 

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Thank you so much.

I'm using the development version of BioC.

Do you mean that I should use the hta20transcriptcluster.db package (without "st")?

If I use the 'release' version of BioC, should I change to another package?

Thank you.

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I tried to be pretty clear. If you are using devel you want the hta20transcriptcluster.db package. If release you want the hta20sttranscriptcluster.db package.

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Thank you so much.

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