Thanks, Stephanie. I am not sure how often things gets updated, but a statement to this effect in the GWASdata documentation would be useful. I am just using the data to learn how to use GWAStools, as well. But using both sets of data together seemed "obvious" and that is how I ran into trouble. --Naomi On 4/16/2014 11:15 AM, Stephanie M. Gogarten wrote: > Hi Naomi, > > Sorry for the delay in responding, I was traveling. The GWASdata > package was made for the sole purpose of running examples for the > GWASTools package, so I would be wary of using it for any other > purposes. I think the Affy and Illumina data sets are not using the > same A/B coding scheme, so switching A and B for the entire data set > will not work - some SNPs will need to be flipped and some will not. > Unfortunately the Affy data does not have annotation for the alleles > used (I inherited the example data from someone else several years > ago, and it didn't come with annotation then). > > The Illumina data does have allele annotation, so you could compare > those samples with 1000 genomes data if you want to investigate SNP > concordance methods. > > Stephanie > > On 4/15/14 8:37 AM, Vincent Carey wrote: >> It did go through. I am not too familiar with these packages. You >> might >> check the 1000 genomes calls to get a third vote, as at least some of >> the >> samples >> should be present in the 1000 genomes VCF. >> >> >> On Tue, Apr 15, 2014 at 8:11 AM, Naomi Altman <naomi at="" stat.psu.edu=""> >> wrote: >> >>> This did not seem to go through the first time. --Naomi >>> >>> >>> -------- Original Message -------- >>> Subject: GWASdata >>> Date: Mon, 14 Apr 2014 14:15:54 -0400 >>> From: Naomi Altman <naomi at="" stat.psu.edu=""> >>> To: Bioconductor mailing list <bioconductor at="" r-project.org=""> >>> >>> >>> >>> I have been trying out some of the SNP tools using the GWASdata data >>> sets. One thing I did was to look for differences in genotype calls >>> between the Affy and Illumina data for what appear to be the same >>> subjects (they have the same subject and family id). They are highly >>> discrepant. At first I thought that the A and B alleles were switched, >>> but swopping the 0's and 2's did not change the magnitude of number of >>> discrepancies. The SNPs appear to be in the same order. >>> >>> Have I misinterpreted something? >>> >>> --Naomi >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at 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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor