[BioC] gc-rma and vsn normalization for rat microarray data

Benilton Carvalho beniltoncarvalho at gmail.com
Sat Jun 12 02:09:46 CEST 2010


I understand I don't offer a vsn() method in oligo (yet), but this can
be easily achieved... Something like the following may get you

cels = list.celfiles()
raw = read.celfiles(cels)
pms = pm(raw)
pmsVSN = vsn::vsnMatrix(pms)
pm(raw) <- pmVSN
rm(pms, pmsVSN)

If any of the other packages offer you a way of normalizing the data
straight from the PM matrices, you can do as I show above...


On 11 June 2010 16:20, Rainer Tischler <rainer_t62 at yahoo.de> wrote:
> Dear all,
> I am analyzing microarray data from an Affymetrix GeneChip Rat ST 1.0 platform, however, since there is no annotation package available that is compatible with the R-package "affy", so far I have only been able to normalize the data using the simple RMA method from the oligo-package. I would like to apply more advanced normalization methods like GC-RMA, VSN, PUMA or BGX, but none of these methods seems to be compatible with the oligo-package.
> Is anybody aware of a possibility to analyze Affymetrix Rat data with the standard affy-package, or alternatively, a possibility to use any of the above normalization methods with the oligo-package?
> Many thanks,
> Rainer
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