Question: How Can I Obtain The Genotype Information For A Particular Snp From Snp6 .Cel Files?
0
gravatar for jh0100x
6.3 years ago by
jh0100x0
jh0100x0 wrote:

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.

microarray • 2.5k views
ADD COMMENTlink modified 3.7 years ago by Biostar ♦♦ 20 • written 6.3 years ago by jh0100x0

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

ADD REPLYlink written 6.3 years ago by Neilfws48k

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

ADD REPLYlink written 6.3 years ago by jh0100x0
1
gravatar for David Quigley
6.3 years ago by
David Quigley11k
San Francisco
David Quigley11k wrote:

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.

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by David Quigley11k
0
gravatar for okko.clevert
6.3 years ago by
okko.clevert220
okko.clevert220 wrote:

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

ADD COMMENTlink written 6.3 years ago by okko.clevert220

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?

ADD REPLYlink written 6.3 years ago by jh0100x0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1172 users visited in the last hour