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Question: Problem with lasso function (ChAMP package)
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gravatar for AST
20 months ago by
AST40
INDIA
AST40 wrote:

Hi all,

I am using champ.lasso() function to detect DMRs in my 450k data, but everytime it is throwing me the following error:

>lasso=champ.lasso (fromFile = FALSE, uploadResults = FALSE, uploadFile = "limma.txt", limma, beta.norm = batchNorm$beta, pd = myload$pd,  filterXY = TRUE, image = TRUE, mafPol.lower = 0, mafPol.upper = 0.05, lassoStyle = "max", lassoRadius = 2000, minSigProbesLasso = 3, minDmrSep = 1000, minDmrSize = 0, adjPVal = 0.05, adjust.method = "BH", resultsDir = paste(getwd(), "results_T", sep = "/"), bedFile = TRUE, DMRpval = 0.05, batchDone = TRUE, normSave)
Run Probe Lasso DMR Hunter
The group labels that have been defined CT do not exist in your sample sheet. Please edit the Sample_Group column or the compare.group parameter. ChAMP will use information in your Sample_group columnn.
[1] "contrast Control Test"
You have found 1637 significant MVPs with a BH adjusted P-value below 0.05
Error in `[.data.frame`(dmr.beta.means, , 22:24, ) : undefined columns selected

Can someone please suggest how can I overcome this problem.

ADD COMMENTlink written 20 months ago by AST40
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