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Normalization of microarray data?

Please help me to pinpoint the error..?

featureData: none
experimentData: use'experimentData(object)'
Annotation: pd.hugene.1.0.st.v1
> normData <- rma(rawData)
Error in (function(classes,fdef,mtable) :
   unable to find an inherited method for function 'probeNames' for signature '"GeneFeatureSet"'
r celfiles rawdata software error
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updated by russhh russhh • written by 12021560-040 12021560-040

You need to give more details if we should help you, e.g. your full command chain, and the output of sessionInfo(). I am guessing that your rawData object is not of the right type, but that is hard to tell from the fragment you posted.

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written by Michael Dondrup Michael Dondrup

1 answer

Just had this as a result of having 'affy' in my namespace by accident

Use the oligo package for your rma method, rather than affy.

Affy::rma converts AffyBatch to ExpressionSet

oligo::rma acts on ExonFeatureSet, ExpressionFeatureSet, GeneFeatureSet, GenericFeatureSet, HTAFeatureSet or SnpCnvFeatureSet; and for the GeneFeatureSet that you've got converts it to ExpressionSet

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written by russhh russhh

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