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 [[alternative HTML version deleted]]