Question: GWASdata
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gravatar for Naomi Altman
5.7 years ago by
Naomi Altman6.0k
Naomi Altman6.0k wrote:
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
snp affy • 552 views
ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by Naomi Altman6.0k
Answer: GWASdata
0
gravatar for Naomi Altman
5.7 years ago by
Naomi Altman6.0k
Naomi Altman6.0k 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@stat.psu.edu> To: Bioconductor mailing list <bioconductor@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]]
ADD COMMENTlink written 5.7 years ago by Naomi Altman6.0k
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@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@stat.psu.edu> > To: Bioconductor mailing list <bioconductor@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@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]]
ADD REPLYlink written 5.7 years ago by Vincent J. Carey, Jr.6.3k
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 >
ADD REPLYlink written 5.7 years ago by Stephanie M. Gogarten740
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
ADD REPLYlink written 5.7 years ago by Naomi Altman6.0k
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