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Sören Gröttrup
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40

@soren-grottrup-3794
Last seen 9.7 years ago

Hi,
I'm trying to compute the copy number for the Illumina 660W-Quad bead
array
with the package crlmm. But for some chromosome it doesn't work and I
get the
following message:
> computeCopynumber(crlmmSetList)
'batch' missing. Assuming all samples in the CrlmmSetList object were
processed together in the same batch.
Fitting model for copy number estimation...
Using 50 df for inverse chi squares.
Sufficient statistics
.
Estimating coefficients
.Called from: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA,
envir =
envir)
Browse[1]>
What shall I do? When I press enter I get:
Error in nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir =
envir) :
Inf values in W or V
> traceback()
5: stop("Inf values in W or V")
4: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir = envir)
3: coefs(plateIndex = p, conf = conf[, plate == uplate[p]], envir =
envir,
CONF.THR = CONF.THR, MIN.OBS = MIN.OBS)
2: .computeCopynumber(chrom = CHR, A = A(ABset), B = B(ABset), calls =
calls(snpset),
conf = confs(snpset), NP = A(NPset), plate = batch, envir =
envir,
SNR = ABset$SNR, bias.adj = FALSE, SNRmin = SNRmin, cdfName =
cdfName,
...)
1: computeCopynumber(crlmmSetList)
What could be the problem? I'm glad for any help.
Thanks in advance
S?ren