[BioC] Affy's 500K SNP arrays - retrieval of probe info

Benilton Carvalho bcarvalh at jhsph.edu
Fri May 25 14:33:15 CEST 2007

Hi An,

I'm assuming you want the offset and GC content for the PM probes, ok?

Say your probe-level data (SnpFeature object) is called "rawData".

theOffset <- pmPosition(get(annotation(rawData)))
theSequences <- pmSequence(get(annotation(rawDataa)))

centralSnps <- which(theOffset == 0)
percentGC <- sapply(gregexpr("G|C", theSequences), length)/25


On May 25, 2007, at 8:00 AM, De Bondt, An-7114 [PRDBE] wrote:

> Dear,
>> From the raw probe level data, we would like to select only those  
>> of the
> central SNP probe (position 0, with the SNP position exactly in the  
> middle)
> from the sense as well as from the antisense strand.  How can we do  
> this?
> We know we can get the GC content from that central probe based on the
> 'Mapping250K_Nsp snp info.txt' file.  How can we get %GC for each  
> of the
> other probes as well? Is there a cdf for the Nsp and Sty arrays? Or  
> can we
> get this info out of the pd.mapping250k.nsp/pd.mapping250k.sty? Or  
> is there
> another way to get that info?
> Thanks in advance for your help!
> Regards,
> An

Benilton Carvalho
PhD Candidate
Department of Biostatistics
Bloomberg School of Public Health
Johns Hopkins University
bcarvalh at jhsph.edu

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