How Can I Obtain The Genotype Information For A Particular Snp From Snp6 .Cel Files?

Question

[jh0100x]

How can I obtain the genotype information for a particular SNP from SNP6 .cel files? So, for e.g. if I wanted to know whether rs12710696 (Affy ID: SNP_A-1856830) is A, G, T or C, can I find this out? If so, how? I can use R or Nexus Copy Number Software.

[Neilfws]

There are multiple packages in R/Bioconductor for working with the SNP6 platform; have you looked at them?

[jh0100x]

Yes but I'm asking specifically how can I obtain genotype information for a given sample for a given SNP?

Answer 1

[David Quigley]

I use CRLMM.

source("http://bioconductor.org/biocLite.R")
biocLite("crlmm")
biocLite("genomewidesnp6Crlmm")
library(crlmm)
path = '/path/to/cels'
cels <- list.celfiles(path, full.names=TRUE)
genders = rep(2, length(cels)) # in my case the CEL files are all female; use 1 for males
cobj = crlmm(cels, row.names=TRUE, col.names=TRUE, probs=c(1/3, 1/3, 1/3), DF=6, SNRMin=5, gender=genders)
call = calls(cobj)
call$MY_CEL_FILE.CEL[ rownames(call)=="rsWhatever" ]

Note that CRLMM will work best with a reasonably large number of CEL files. Just one alone won't cut it. See documentation for more details.

Answer 2

[okko.clevert]

If you only want to check a few SNPs I would use the NetAffx center at Affymetrix, otherwise the pd.genomewidesnp.6 in Bioconductor...

[jh0100x]

But this doesn't check the actual SNP genotyping calls in my data, does it? How can I check whether sample XXXX has an A, G, T or C at rs12710696?