[R] SNPRelate: Plink conversion

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

Re: [R] SNPRelate: Plink conversion

...@hotmail.com CC: r-help@r-project.org 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

[R] SNPRelate- problem performing PCA

Hi, I have a dataset containing approximately 2 million SNPs. The data is in PLINK format. The data conversion was successful except for a warning message Nan introduced due to coercion. My problem is that I get an error message when I perform a PCA: Principal Component Analysis (PCA) on SNP