[BioC] crlmm - computeCopynumber error

Christian Ruckert cruckert at uni-muenster.de
Thu Apr 23 19:13:57 CEST 2009

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.


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