User: Nastasia

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Nastasia0
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Posts by Nastasia

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Comment: C: Finding DMRs using dmrFinder in bsseq
... I used the same commands for chromosome 16 and for chromosome 20. I post here the commands for chromosome 16. list.files(pattern="*.cov") -> cov.files read.bismark(files=cov.files,sampleNames=gsub(".cov","",cov.files),rmZeroCov=TRUE, strandCollapse=FALSE) ->bsseq.data bsseq.data[[1]] <- c ...
written 1 hour ago by Nastasia0
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Answer: A: Finding DMRs using dmrFinder in bsseq
... Yes, thank you! I sent a link to you by e-mail. There are COV-files for 16 chromosome (and for example for 20 chromosome) in the folder. Files with "n" letter refer to the normal tissue group, files with "t" letter refer to the tumor tissue group. So, I compare the two groups of 6 samples each. ...
written 2 days ago by Nastasia0
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Comment: C: Finding DMRs using dmrFinder in bsseq
... Dear Dr. Hickey, It's all right when I'm analyzing chromosomes 17-22. But when analyzing the 16 chromosomes, I see the following error when calling the function BSmooth.tstat: Error in preplot.locfit.raw(object, newdata, where, what, band):     NA/NaN/Inf in foreign function call (arg 2) In additio ...
written 4 days ago by Nastasia0
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Comment: C: Finding DMRs using dmrFinder in bsseq
... Thank you very much for your answer! ...
written 7 days ago by Nastasia0
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Comment: C: Finding DMRs using dmrFinder in bsseq
... Excuse me, yes, it's true. ...
written 7 days ago by Nastasia0
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Comment: C: Finding DMRs using dmrFinder in bsseq
... Thank you for your consideration! 1. I tryed to change parameters ns (minimum number of meth.loci in a smoothing window) and h (minimum smoothing window). The value of ns is equal 70 by default. The above warnings are not occure when I set the meaning of ns to 700 or 800 or more. At the same time, l ...
written 7 days ago by Nastasia0
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Finding DMRs using dmrFinder in bsseq
... Hello! Could you help me with my challenges? I have paired-end data obtained with RRBS expriment. I did the adapter and quality trimming using trim_galore. Then i the read alignments the methylation extraction using Bismark . And farther I worked with the produced coverage files, is it all right? = ...
bsseq r package written 7 days ago by Nastasia0

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