Hi,
I would like to use justRMA() in R/bioconductor using a remapped affymetrix CDF for u133a and u133aplus2.0 chips. I'd like to figure out how to ensure that I get an annotated expression set as I would using the affymetrix CDFs.
Thanks for your help.
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written
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Sam •
Do you mean you don't want to use the existing Bioconductor packages, you want to build one from your own custom CDF file? If so, then maybe makecdfenv
I think that [?] is asking about remapping probes for the regular HG-U133A and HG-U133plus2 arrays, not about custom array designs.
@unknown: being as precise as possible when formulating the question can only help you getting a precise answer. Now that is appears clear that you are after alternative mapping, what is exactly "just can't seem to get them to work" ?
You can browse the latest release versions of the CDF files here
To install the latest release CDF for affy 133 a plus2.0:
source("http://bioconductor.org/biocLite.R")
biocLite("hgu133plus2.db")
I think the affy package will go out and get the latest CDF for you if you don't have one installed already.
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written
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David Quigley
The MBNI's CDF might be an easy entry point to the world of remapped CDFs for Affymetrix.
The use of alternative probe-probeset mappings was mentioned in the answer to an other question.
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written
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Laurent Gautier
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