Question: Normalization of microarray data?
1
gravatar for 12021560-040
3.6 years ago by
12021560-04060
Pakistan
12021560-04060 wrote:

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"'
rawdata software error R celfiles • 2.0k views
ADD COMMENTlink modified 3.1 years ago by russhh4.9k • written 3.6 years ago by 12021560-04060
2

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.

ADD REPLYlink written 3.6 years ago by Dr. Mabuse47k
3
gravatar for russhh
3.1 years ago by
russhh4.9k
UK, U. Glasgow
russhh4.9k wrote:

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

ADD COMMENTlink written 3.1 years ago by russhh4.9k
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