Hi All,
 
I am trying to filter Illumina human methylation data using nsFilter/ featureFilter, but keep getting the error "Invalid subscript type list".
 
The M values were read as an expression set and the annotation (IlluminaHumanMethylation450k),  phenodata (as annotated dataframe) and feature data (as annotated dataframe) were assigned to it. 
................................my expression set....................................
>dataM
ExpressionSet (storageMode: lockedEnvironment)
assayData: 467115 features, 96 samples
   elementnames: exprs
protocolData: none
phenoData
     rowNames: X111111_A.... (96 total)
varMetaData: labelDescription
featureData
   featureNames: cg00000029....(467115 total)
fvarLabels: V1
fVarMetadata:labelDescription
experimentData: use 'experimentData(object)'
Annotation: IlluminaHumanMethylation450k
 
****************************************************
 
The command I tried were simply: nsFilter(dataM, require.entrez=TRUE)
And the same with featureFilter.
 
Any clue on what is causing this error would be most helpful.
 
Thanks in advance,
 
Hajja
 
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