Hi, I have genotyped samples from Affy6.0 platform using crlmm algorithm from Oligo and I am facing difficulties in interpretation. I am trying to match the SNP calls from crlmm with their respective alleles. 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? I used the code provided in the oligo package help. I would greatly obtain a result in a tabulated file like below: NA06985.CEL NA06991.CEL SNP_A-1507972 TT TC SNP_A-1510136 AG GG Thanks -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] pd.genomewidesnp.6_1.10.0 RSQLite_0.11.4 [3] DBI_0.2-7 oligo_1.24.0 [5] Biobase_2.20.1 oligoClasses_1.22.0 [7] BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affxparser_1.32.3 affyio_1.28.0 BiocInstaller_1.10.2 [4] Biostrings_2.28.0 bit_1.1-10 codetools_0.2-8 [7] ff_2.2-11 foreach_1.4.1 GenomicRanges_1.12.4 [10] IRanges_1.18.1 iterators_1.0.6 preprocessCore_1.22.0 [13] splines_3.0.1 stats4_3.0.1 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.