[GenABEL-dev] Error message in GenABEL

[Yurii Aulchenko]

Ok, nice little problem!

We will probably be able to add such feature really quickly when having a little piece of time (can someone file in feature request?)... Which probably may mean up to 1 week from now.

Yurii

On Thu, 16 Dec 2010 11:36:35 +0100, Østensen,_Ingrid_Helen_Garmann wrote:
> Hi
> 
> I tested what you wrote and it works, the same does: descriptives.marker(ge03d2ex, idsubset =20(ge03d2ex at phdata$dm2=1))
> 
> But now I have gotten a bigger problem. I have tried to read a dataset from GenomeStudio but it does not work. I think the reason is that Illumina codes missing geno> 
> If not all genotypes for a SNP is missing I get this error message:
> 
> ## One or more genotype is coded NC (no-call)
> > convert.snp.illumina(inf="TestData_miniSett_081210.txt", out =20"utTest.raw", strand =20"+")
> Reading genotypes from file 'TestData_miniSett_081210.txt' ...
> Error in convert.snp.illumina(inf =20"TestData_miniSett_081210.txt", out =20"utTest.raw",  : 
>   illegal genotype (three alleles) for SNP 'rs9999030' (line 3)!
> 
> If all genotypes for a SNP is missing I get this error message:
> ## All genotypes for a SNP is coded NC (no-call)  
> > convert.snp.illumina(inf="TestData_LiteSett_081210_3.txt", out =20"utTest2.raw", strand =20"+")
> Reading genotypes from file 'TestData_LiteSett_081210_3.txt' ...
> Error in convert.snp.illumina(inf =20"TestData_LiteSett_081210_3.txt",  : 
>   coding 'CN' for SNP not recognised !
> 
> Is there a way of getting GeneABEL to take other values for missing or do I have to find a way of replacing the NC with 00 or --?
>=2> Regards,
> Ingrid
> 
> 
> -----Original Message-----
> From: Yurii S. Aulchenko [mailto:i.aoultchenko at erasmusmc.nl] 
> Sent: 06 December 2010 17:33
> To: =?ISO-8859-1?Q?"Østensen; Østensen, Ingrid Helen Garmann
> Subject: Re: Error message in GenABEL
> 
> can you please try
> 
> names(phdata(ge03d2ex))
> descriptives.marker(ge03d2ex, ids =20(phdata(ge03d2ex)$dm2 = 0))
> descriptives.marker(ge03d2ex, ids =20which(phdata(ge03d2ex)$dm2 = 0))
> descriptives.marker(ge03d2ex[which(phdata(ge03d2ex)$dm2 = 0),])
> 
> and let me know
> 
> On Dec 2, 2010, at 11:12 AM, Østensen, Ingrid Helen Garmann wrote:
> 
> > Hi
> >
> > I am not sure to send this e-mail to you or any of the R/ 
> > Bioconductor help list so I thought I start at this end.
> >
> > I am building a script for analyzing GWA data using GenABEL and what  
> > I learned at ERASMUS summer course but I get an error message that I  
> > can not find a solution on:
> >
> > > descriptives.marker(ge03d2ex,> > Error in data at gtdata[idsubset, ] :
> >   error in evaluating the argument 'i' in selecting a method for  
> > function '['
> >
> >
> > I am using the dataset that are in GenABEL and it has worked fine so  
> > far:
> > library(GenABEL)
> > data(ge03d2ex)
> >
> >
> >
> > Here is my session information:
> > > sessionInfo()
> > R version 2.12.0 (2010-10-15)
> > Platform: i386-pc-mingw32/i386 (32-bit)
> >
> > locale:
> > [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United  
> > Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
> > [4] LC_NUMERIC=C                            LC_TIME=English_United  
> > Kingdom.1252
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] GenABEL_1.6-4 MASS_7.3-8
> >
> > loaded via a namespace (and not attached):
> > [1] tools_2.12.0
> >
> > Any suggestions?
>=> > Regards,
> > Ingrid
> >
> > ---------
> > Ingrid H.G. Østensen
> > Researcher/bioinformatician
> > The Norwegian Institute of Public Health
> >
> > E-mail: ingrid.ostensen at fhi.no
> > Phone: 0047 21 07 83 03
> >
> > Visiting addresses:
> > Marcus Thranes gate 6, 0473 Oslo, Norway
> >
> > Postal addresses:
> > Norwegian Institute of Public Health
> > P.O.Box 4404 Nydalen
> > N-0403 Oslo
> > Norway
> >
> 
> -----------------------------------------------------------
> Yurii Aulchenko
> Erasmus MC Rotterdam
> Department of Epidemiology, Ee 2200
> Postbus 2040, 3000 CA Rotterdam
> The Netherlands
> 
> phone: +31107043486
> fax: +31107044657
> 
> 
> 
> 
> 

--
Yurii Aulchenko (sent from my mobile device)