User: Daniel E. Weeks

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Posts by Daniel E. Weeks

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Comment: C: package 'ChAMP' demo/test code fails at champ.CNA()
... But it looks like in champ.MVP (which is called by champ.lasso), it is expected (but not required) that the Sample_Group column contains the codes "C" and "T" for 'controls' and 'cases'.   > champ.MVP function (beta.norm = myNorm$beta, pd = myLoad$pd, adjPVal = 0.05, adjust.method = "BH", ...
written 3.3 years ago by Daniel E. Weeks0
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Answer: A: ChAMP input: Beta Matrix?
... Look at the help page for champ.process(). Looks to me like you should do this: champ.process(fromIDAT=FALSE, fromFile=TRUE) and then it will try to read the data in from 'beta.txt' and 'sampleSheet.txt' > ChAMP:::champ.read function (betaFile = "beta.txt", sampleSheet = "sampleSheet.txt", ...
written 3.3 years ago by Daniel E. Weeks0
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ChAMP ComBat step error: Error in if (min(beta.c) == 0) { : missing value where TRUE/FALSE needed
... When trying to run ChAMP version 1.8.2 on a data set of 91 samples using the default champ.process command, it got through the SVD step, but then died at the ComBat step: Preparing files for ComBat Error in if (min(beta.c) == 0) { : missing value where TRUE/FALSE needed Calls: champ.process -> ...
champ methylation illumina450k written 3.3 years ago by Daniel E. Weeks0

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