Doesn't this belong on Bioconductor rather than here? -- Bert
On Fri, Nov 8, 2013 at 6:04 AM, Danica Fabrigar <danica_...@hotmail.com> wrote: > Hi, > > Following my earlier posts about having problems performing a PCA, I have > worked out what the problem is. The problem lies within the PLINK to gds > conversion. > > It seems as though the SNPs are imported as "samples" and in turn, the > samples are recognised as SNPs: > >>snpsgdsSummary("chr2L") > Some values of snp.position are invalid (should be > 0)! > Some values of snp.chromosome are invalid (should be finite and >=1)! > Some of snp.allele are not standard! E.g, 2/-9 > The file name: chr2L > The total number of samples: 2638506 > The total number of SNPs: 67 > SNP genotypes are stored in SNP-major mode. > The number of valid samples: 2638506 > The number of valid SNPs: 0 > > > Anyone have any ideas on how to fix this? > > Thanks, > Danica > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.