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
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
> 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]]
