fRMA error - unable to create unique mapping
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yesitsjess • 0
@yesitsjess-11565
Last seen 4.8 years ago
library(affy)
library(frma)
install.packages("hgu133plus2hsentrezgcdf_15.0.0.tar.gz", repos=NULL, type="source")
data <- ReadAffy(cdfname="HGU133Plus2_Hs_ENTREZG")
object <- frma(data)
Error in frmaAffyBatch(object, background, normalize, summarize, input.vecs,  :
  Mismatch between pmindex(object) and names of input.vecs and unable to create unique mapping.

It's been a long time since I processed array data and I could really do with some advise for resolving this error.

frma frmatools affy • 1.0k views
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@james-w-macdonald-5106
Last seen 2 days ago
United States

The frozen RMA estimates for that array are based on the conventional probe -> probeset mappings, not the MBNI re-mapped probeset definitions. If you want to use frma, you need to use the conventional cdf.

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@matthew-mccall-4459
Last seen 2.4 years ago
United States

There are frozen parameters for one alternative probe mapping. To find out the alternative CDF version that is currently available, you can do the following:

library(hgu133plus2frmavecs)
data(hgu133plus2hsentrezgfrmavecs)
hgu133plus2hsentrezgfrmavecs$version

It looks like you were using hgu133plus2hsentrezgcdf_15.0.0 when the alternative CDF version that matches the current frmavecs is hgu133plus2hsentrezgcdf_19.0.0.

Hope that helps.

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Thanks for clarifying, Matthew. It is working, indeed. Flawlessly. Haven't tried with the exon arrays, though. Will it still work?

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Yes, it will work for exon arrays as well. However, you need to use the oligo package (rather than the affy package) to read in the CEL files. 

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