Hi,
I am trying to analysis SNP6.0 copy number data. For this purpose I am using the crlmm package in R. The first steps look like;
cnSet <- constructAffyCNSet(sinfo$celFiles, batch=rep(1, nrow(sinfo)),cdfName="genomewidesnp6",
genome="hg19")
cnrmaAffy(cnSet)
snprmaAffy(cnSet)
validCEL(sinfo$celFiles)
genotypeAffy(cnSet)
All the lines pass properly except the genotypeAffy function that returns:
Error in crlmmGT2(A = A(cnSet), B = B(cnSet), SNR = cnSet$SNR, mixtureParams = cnSet@mixtureParams, : No arrays above quality threshold!
Do you have any idea, how can I resolve this issue?
1 answer
Check some of the parameters that can be passed to genotypeAffy(), namely, these: https://www.rdocumentation.org/packages/crlmm/versions/1.30.0/topics/genotypeAffy
How many samples have you got? What is the source tissue? If it is something like FFPE DNA, then many probes will fail.
That is a low number. Take a look at the parameters that can be passed to the function.
Thank you. I checked these parameters. Now I increased the number of samples to 80 and I get just a warning:
Warning message:
In crlmmGT2(A = A(cnSet), B = B(cnSet), SNR = cnSet$SNR, mixtureParams = cnSet@mixtureParams, :
Recalibration not possible. Possible cause: small sample size.
is it still a problem?
Yes and no... the issue is now the parameter recallRegMin=1000. I would reduce that progressively until the warning diappears; however, if you get below, e.g., 500, then start to worry...
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