> Message: 19
> Date: Thu, 23 Apr 2009 19:13:57 +0200
> From: Christian Ruckert <cruckert@uni-muenster.de>
> Subject: [BioC] crlmm - computeCopynumber error
> To: bioconductor@stat.math.ethz.ch
> Message-ID: <49F0A1D5.5030202@uni-muenster.de>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
> I get an error for some chromosomes when running function
>
> computeCopynumber(chrom=i, A=A, B=B, calls=genotypes, conf=conf,  
> NP=NP,
> plate=plate, envir=env, DF.PRIOR=50, MIN.OBS=1, SNR=SNR,  
> SNRmin=SNRmin)
>
> from package crlmm. The output is:
>
> Sufficient statistics
> .
> Estimating coefficients
> .
> Allele specific copy number
> .
> Copy number for nonpolymorphic probes...
> .Error in crossprod(X[ix, ]) : object 'ix' not found
>
>
> The error origins in function nonpolymorphic in lines
>
> if (nrow(X) > 5000)
>         ix <- sample(1:nrow(X), 5000)
>     betahat <- solve(crossprod(X[ix, ]), crossprod(X[ix, ], Y[ix]))
>
> It seems, that ix is not initialized if nrow(X) < 5000.
>
>
> Regards,
> Christian

This error should be fixed in crlmm version 1.3.1.  Thanks-

Rob


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