Using Custom Cdfs In R

Question

[Sam]

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.

Answer 1

[Cassj]

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

[Laurent Gautier]

I think that [?] is asking about remapping probes for the regular HG-U133A and HG-U133plus2 arrays, not about custom array designs.

[Sam]

ya examples being affyprobeminer or brainarray provided CDFs. i just can't seem to get them to work.

[Laurent Gautier]

@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" ?

Answer 2

[David Quigley]

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.

Answer 3

[Laurent Gautier]

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.