Hi friends,

I'm analyzing an affymetrix array data, however during normalization step, I faced the error with both affy and oligo. I used the bellow code

x <- read.table('data.txt',header = TRUE, sep = '\t', stringsAsFactors = FALSE, fill=TRUE)
probes <- x$ID_REF
x <- data.matrix(x[,2:ncol(x)])
rownames(x) <- probes

exp <-affy::rma(x)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘probeNames’ for signature ‘"matrix"’

exp <-oligo::rma(x)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘rma’ for signature ‘"matrix"’

Here is the head of data:

> head(x[,1:4])

           GSM11158 GSM11159 GSM11160 GSM11161
 A01157cds_s_at   573.85   461.88   496.66   540.91
A03913cds_s_at  1393.33  1348.11  1512.08  1750.25
A04674cds_s_at   846.13   924.19   964.13  1002.45
A07543cds_s_at   553.83   391.08   537.27   543.64
A09811cds_s_at   980.42  1054.19  1141.65  1214.16
A16585cds_s_at   665.35   678.20   706.09   784.31

Could you please help me out how to solve the issue?

Thanks

Your error is because the affy::rma() function is expecting an AffyBatch object not a matrix. You can check that by taking a look at the help file for rma with ?affy::rma.

As an aside, most data on GEO has already been processed, and I'm not sure you necessarily want to be applying rma to it again if it's already been normalised, but I haven't read anything about this specific dataset.

I wonder if it would be easier to use GEOquery to get this data directly, and then you end up with an ExpressionSet you can feed into many other Bioconductor packages. You can get the data from GEO with:

x <- GEOquery::getGEO('GSE738')
x
#  assayData: 8740 features, 46 samples 
#    element names: exprs 
#  protocolData: none
#  phenoData
#    sampleNames: GSM11158 GSM11159 ... GSM11203 (46 total)
#    varLabels: title geo_accession ... data_row_count (30 total)
#    varMetadata: labelDescription
#  featureData
#    featureNames: A01157cds_s_at A03913cds_s_at ... Z96106_at (8740 total)
#    fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
#    fvarMetadata: Column Description labelDescription
#  experimentData: use 'experimentData(object)'
#    pubMedIds: 18629135 
#  Annotation: GPL85