[BioC] Human Gene 1.1 ST cdf

[Michal Blazejczyk]

Hi Nicolas,

There was a thread here about two weeks ago that discussed this specific question.

The question was:

> I have noticed that Bioconductor's just.rma() function returns fewer transcript-level
> probesets that RMA in APT for the Human Gene 1.0 ST array.  To be specific, 819 probesets
> are missing, and most of them seem to be "real", i.e. they are annotated when I run them
> through NetAffx.

And one of the responses was:

> in just.rma and rma, it was assumed that each probe could be in at most 1 probeset.
> once a probe was used, it cannot be reused. on the ST arrays, some probes can be in many
> probesets... so if you use rma, eventually, all the probes in a probeset have been used
> once by the time the current probeset needs it & you get NA's.

Best,

Michał Błażejczyk
McGill University and Genome Quebec Innovation Centre
http://www.gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=e



> Thanks Jim.
> I found a cdf on BrainArray
> http://www.affymetrix.com/browse/products.jsp?navMode=34000&productId=131554&navAction=jump&aId=productsNav#1_1
> Then I plan to simply use the RMA function from the affy package.
>
> require(hugene11stv1hsentrezgcdf)
> require(hugene11stv1hsentrezg.db)
> require(hugene11stv1hsentrezgprobe)
> cdfname <- "hugene11stv1hsentrezg"
> abatch <- ReadAffy(celfile.path=rawDataDir, cdfname=cdfname)
> rmaData <- rma(abatch, cdfname = cdfname)
>
> Is there still some reason to use xps or oligo instead of the affy
> package ?
> The vignette of oligo seems to also use RMA ...
> http://www.bioconductor.org/packages/2.7/bioc/vignettes/oligo/inst/doc/V5ExonGene.pdf
>
> Thanks
> Nicolas