crlmm - computeCopynumber error
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@christian-ruckert-3294
Last seen 4.9 years ago
Germany
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
crlmm crlmm • 852 views
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@christian-ruckert-3294
Last seen 4.9 years ago
Germany
Vincent Carey schrieb: > please provide your sessionInfo() > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-pc-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] genomewidesnp6Crlmm_1.0.2 affy_1.22.0 [3] Biobase_2.4.0 crlmm_1.2.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.6.0 DBI_0.2-4 RSQLite_0.7-1 [4] affyio_1.12.0 annotate_1.22.0 genefilter_1.24.0 [7] mvtnorm_0.9-5 preprocessCore_1.6.0 splines_2.9.0 [10] survival_2.35-4 xtable_1.5-5
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Rob Scharpf ▴ 250
@rob-scharpf-1931
Last seen 9.7 years ago
> 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 [[alternative HTML version deleted]]
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