[BioC] how to read in affy snp 500K arrays

[affy snp]

Hi Benilton,

Thanks for the note. What I intended to do is to
get the intensity data from Affy SNP cel files and
do copy number analysis.

So for oligo, after snprma(), I can take the ave of the
two strand and then accomplish what I said in the above?

Best,
    Allen

On Nov 9, 2007 11:29 PM, Benilton Carvalho <bcarvalh at jhsph.edu> wrote:
> oligo doesn't "produce" data on both strands, per se. :-)
>
> The data are given on both strands, for some SNPs on the 500K array
> set. If one uses snprma(), oligo *summarizes* these data to the
> SNP-allele-strand level.
>
> It's a little bit hard to say what to do, when we don't know what it's
> going to be used for...
>
> An ad-hoc method for summarization to the SNP-Allele level can be
> achieved by taking the average log-intensities across strands; or one
> can choose to manually run a summarization algorithm (say
> median-polish) on the SNP-allele sets (a la RLMM).
>
> Cheers,
>
> b
>
>
> On Nov 8, 2007, at 9:51 PM, affy snp wrote:
>
> > Hi Ben,
> >
> > I checked it out and found oligo would produce data for two strands,
> > sense and anti-sense.
> > Is there a way to somehow combine the two type of datawhich will make
> > sense?
> >
> > Thank-you!
> >
> > Allen
> >
> >
> > On 11/8/07, Benilton Carvalho <bcarvalh at jhsph.edu> wrote: check the
> > oligo package, but you also need to download the data
> >> packages for the arrays you're using:
> >>
> >> pd.mapping250k.sty
> >> pd.mapping250k.nsp
> >>
> >> b
> >>
> >> On Nov 8, 2007, at 9:34 PM, affy snp wrote:
> >>
> >> > Dear list,
> >> >
> >> > I am analyzing a bag of Affy SNP 500K arrays and would like to
> >> > know which package can be used to read in the raw .CEL files
> >> > and get the intensity values. In other words, I am looking for
> >> > the function like:
> >> >
> >> > library(affy)
> >> > mydata <- ReadAffy()
> >> > eset_rma <- rma(mydata)
> >> >
> >> > provided by affy package to analyze affy gene expression data.
> >> >
> >> > Thank you very much!
> >> >
> >> > Sincerely,
> >> > Allen
>