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haowulab / DSS

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error with DMLtest in DSS (DNA methylation analysis) #45

Closed shaghayeghsoudi closed 2 months ago

shaghayeghsoudi commented 2 months ago

Hi DSS developers. Thanks so much for the package. We have started using DSS to find DML/DMR for our RRBS data obtained from normal, primary and relapse sarcoma human tumors.

For now I am running DSS for two-group comparisons (for example to find DMLs/DMRs between Normal and primary tumors).

I should mentioned the number of replicates are not equal. For example I have 110 primary tumors and only 70 normal samples. When I run DML test with the following code

dmlTest <- DMLtest(BSobj, group1=groupNormal, group2=groupPrimary, smoothing=TRUE)

I keep getting this error message:

In shrk.phi[ix] <- shrk.phi2 :
 number of items to replace is not a multiple of replacement length

I do not know where the error is coming from. I believe I do not have any "NA" in my data set. So I wanted to ask is there any clue on why I am getting this error message?

Thanks you very much

haowulab commented 2 months ago

Hmm, we never encountered this problem before. Without debugging it's very difficult for me to figure out. Does this happen when analyzing a particular chromosome?

shaghayeghsoudi commented 2 months ago

Hi, thanks for your reply. I am analyzing all chromosomes together. But when I subset the data (for example the fist 10K positions) it goes fine. But it happens when I take large subset such as 100K. Is there any chance I could share subset of my samples with you to have a look?? I have checked all possible scenarios that may cause this error but have not found anything so far. Thank you very much