Question: fRMA error - unable to create unique mapping
0
gravatar for yesitsjess
3.1 years ago by
yesitsjess0
yesitsjess0 wrote:
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.

affy frma frmatools • 769 views
ADD COMMENTlink modified 3.1 years ago by Matthew McCall830 • written 3.1 years ago by yesitsjess0
Answer: fRMA error - unable to create unique mapping
0
gravatar for James W. MacDonald
3.1 years ago by
United States
James W. MacDonald51k wrote:

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.

ADD COMMENTlink written 3.1 years ago by James W. MacDonald51k
Answer: fRMA error - unable to create unique mapping
0
gravatar for Matthew McCall
3.1 years ago by
United States
Matthew McCall830 wrote:

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.

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Matthew McCall830

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

ADD REPLYlink written 2.6 years ago by lcordeiro0

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. 

ADD REPLYlink written 2.6 years ago by Matthew McCall830
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