Dear Bioconductors, I have genotyped 8 samples from Affy6.0 platform using crlmm algorithm from Oligo and I am facing difficulties in interpretation. I am trying to match the gender from the phenodata with the SNP calls from crlmm on X and Y chromosomes. I would appreciate any comments and help. Given a SNP has A and B allele, is it that A is always a major allele and B is always a minor allele or is it that the allele A and B are alphabetically assigned; the first alphabet (A,T,G,C) gets assigned as A allele and the next alphabet is assigned as B allele? Another question is how do I differentiate between a AA genotype and just A (no copy from the other parent). Are they both coded as AA and given a call of 1 or 3? Here is my code: crlmmCalls <- readSummaries("calls", outDir) conn <- db(pd.genomewidesnp.6) sql <- "select man_fsetid,dbsnp_rs_id,chrom from featureSet where chrom='X' " X_snps <- dbGetQuery(conn, sql) tmp <- rownames(crlmmCalls) %in% X_snps$man_fsetid ## Get crlmmCalls for X snps for 8 samples tmp <- crlmmCalls[tmp,] tmp[tmp[,6] == 3 & tmp[,7] == 1,] ## 2 male genotypes This gives thousands of SNPs which is weird. Considering if the SNP has a genotype of 1 its AA, if 2 its AB, if 3 its BB. How come the 2 men have a homozygous AA,BB calls for the X chrom SNPs? Should not most of the SNPs (other than the homologous X and Y regions) be heterozygous?. What might be the problem? > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.genomewidesnp.6_0.4.2 RSQLite_0.8-3 DBI_0.2-5 [4] oligo_1.10.3 preprocessCore_1.8.0 oligoClasses_1.8.0 [7] Biobase_2.6.1 loaded via a namespace (and not attached): [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.12 IRanges_1.4.13 [5] splines_2.10.1 tools_2.10.1 Thank you

the definition of allele A and allele B is on the allele_a, allele_b columns of the database. differentiating between AA and A calls is currently out of scope for crlmm. If you use the crlmm package, as previously suggested, you will be able to use also the copy number tool that may improve your findings. about the calls on chrX for males, i assume you 100% sure about the gender of the samples, right? the algorithm does not call genotypes conditionally on gender, so this may be the reason you're observing this. how does this look like when you use the crlmm package instead (recommended for SNP 5.0 and SNP 6.0 arrays)? b On Mon, Apr 5, 2010 at 9:07 PM, jeremy wilson <jeremy.wilson88 at="" gmail.com=""> wrote: > Dear Bioconductors, > > I have genotyped 8 samples from Affy6.0 platform using crlmm algorithm > from Oligo and I am facing difficulties in interpretation. I am trying > to match the gender from the phenodata with the SNP calls from crlmm > on X and Y chromosomes. I would appreciate any comments and help. > Given a SNP has A and B allele, is it that A is always a major allele > and B is always a minor allele or is it that the allele A and B are > alphabetically assigned; the first alphabet (A,T,G,C) gets assigned as > A allele and the next alphabet is assigned as B allele? > > Another question is how do I differentiate between a AA genotype and > just A (no copy from the other parent). Are they both coded as AA and > given a call of 1 or 3? > > Here is my code: > > crlmmCalls <- readSummaries("calls", outDir) > conn <- db(pd.genomewidesnp.6) > sql <- "select man_fsetid,dbsnp_rs_id,chrom from featureSet where chrom='X' " > X_snps <- dbGetQuery(conn, sql) > tmp <- rownames(crlmmCalls) %in% X_snps$man_fsetid ?## Get crlmmCalls > for X snps for 8 samples > tmp <- crlmmCalls[tmp,] > tmp[tmp[,6] == 3 & tmp[,7] == 1,] ? ## ? 2 male genotypes > > This gives thousands of SNPs which is weird. > > > Considering if the SNP has a genotype of 1 its AA, if 2 its AB, if 3 > its BB. How come the 2 men have a homozygous AA,BB calls for the X > chrom SNPs? Should not most of the SNPs (other than the homologous X > and Y regions) be heterozygous?. > > What might be the problem? > > >> sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-pc-linux-gnu > > locale: > ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 > ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 > ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] pd.genomewidesnp.6_0.4.2 RSQLite_0.8-3 ? ? ? ? ? ?DBI_0.2-5 > [4] oligo_1.10.3 ? ? ? ? ? ? preprocessCore_1.8.0 ? ? oligoClasses_1.8.0 > [7] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affxparser_1.18.0 ?affyio_1.14.0 ? ? ?Biostrings_2.14.12 IRanges_1.4.13 > [5] splines_2.10.1 ? ? tools_2.10.1 > > > Thank you >