Hi Bert,
I thought it was suitable to post the question on the R mailing list first seeing as the problem/question is related to an R package.....

Danica



> Date: Fri, 8 Nov 2013 08:14:03 -0800
> Subject: Re: [R] SNPRelate: Plink conversion
> From: gunter.berton@gene.com
> To: danica_714@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_714@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
 		 	   		  
	[[alternative HTML version deleted]]

