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 data which will make 
> sense?
>  
> Thank-you!
>  
> Allen
>
>  
> On 11/8/07, Benilton Carvalho <bcarvalh@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

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