Hi Sean, Thanks for the quick response. I have both for the same sample but I am interested in expresssion analysis. Should I sum up all the SNP reads? Jiang On Tue, Dec 18, 2012 at 2:08 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > On Tue, Dec 18, 2012 at 1:57 PM, zhengyu jiang <zhyjiang2006@gmail.com>wrote: > >> Hi there, >> >> I am trying to deal with SNPs in the two channel >> beadchip microarray expression analysis. Does anyone know how >> to calculate the expression of some genes with SNPs (heterozygotes or >> homozygotes)? Is there any package for this? >> This is probably an old question but I cannot find the answer from google. >> > > Hi, Jiang. > > Could you clarify what data types you have? Do you have SNP/genotype > data? Do you have gene expression data? Are these data on the same > samples? > > Sean > > [[alternative HTML version deleted]]

I was wondering if anyone is familiar with this case. Thanks, On Tue, Dec 18, 2012 at 2:48 PM, zhengyu jiang <zhyjiang2006@gmail.com>wrote: > Hi Sean, > QTL analysis is actually not what I mean. > > I am asking about microarray data analysis. For example, for a particular > gene M, it has two 2 alleles targeted by 2 probes on the microarray - one > contains genotype "A" & the other contains genotype "G" . After microarray > hybrydization, I got both signals for the two probes. Should I sum up all > the signals in order to get a number for this gene? Or is there any other > algrithm/package to deal with such situation? > > I see--RNA on the SNP array. Sorry for my confusion. I have not dealt with that situation myself, so I cannot comment directly. Perhaps someone has experience with this application can give a good answer about how best to move forward. Sean > On Tue, Dec 18, 2012 at 2:25 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > >> >> >> On Tue, Dec 18, 2012 at 2:14 PM, zhengyu jiang <zhyjiang2006@gmail.com>wrote: >> >>> Hi Sean, >>> Thanks for the quick response. I have both for the same sample but I am >>> interested in expresssion analysis. Should I sum up all the SNP reads? >>> >>> >> I'm not sure what you mean by "SNP reads". However, you might want to >> look at the GGtools package for looking into eQTL analysis which is, it >> seems, what you are interested in doing. >> >> Sean >> >> >> >>> Jiang >>> >>> On Tue, Dec 18, 2012 at 2:08 PM, Sean Davis <sdavis2@mail.nih.gov> >>> wrote: >>> >>> > >>> > >>> > On Tue, Dec 18, 2012 at 1:57 PM, zhengyu jiang <zhyjiang2006@gmail.com>>> >wrote: >>> > >>> >> Hi there, >>> >> >>> >> I am trying to deal with SNPs in the two channel >>> >> beadchip microarray expression analysis. Does anyone know how >>> >> to calculate the expression of some genes with SNPs (heterozygotes or >>> >> homozygotes)? Is there any package for this? >>> >> This is probably an old question but I cannot find the answer from >>> google. >>> >> >>> > >>> > Hi, Jiang. >>> > >>> > Could you clarify what data types you have? Do you have SNP/genotype >>> > data? Do you have gene expression data? Are these data on the same >>> > samples? >>> > >>> > Sean >>> > >>> > >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > [[alternative HTML version deleted]]