User: yuping.zhang

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Posts by yuping.zhang

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Answer: A: problem with identifySigDMR command
... After looking into the code, I change two lines in the part of "check the gaps of sparse probe" and think it works.      ## check the gaps of sparse probe     gaps.i <- which(c(FALSE, diff(allPosition.i) > maxGap) & status.i == 1)     # the gap should be 1 in both sides     gaps.i <- g ...
written 20 months ago by yuping.zhang0
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problem with identifySigDMR command
... I found methyAnalysis is a pretty nice tool after testing several packages for the same purpose.  But recently I found an issue. I used default setting to identify significant DMRs,  so the maximum gap allowed between two nearby probes should be no more than 2000. But why the resultant DMRs includin ...
methyanalysis written 21 months ago by yuping.zhang0
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conflicts in chromosome number
... Hi, I feel the chromosome information is wrong in the output of the cpg.annotate command.  Could you check what's wrong here? > summary(as.factor(myannotation1$CHR))     1     2     3     4     5     6     7     8     9    10    11    12    13    14    15    16    17    18    19    20    21    ...
dmrcate written 22 months ago by yuping.zhang0 • updated 22 months ago by Tim Peters70
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error when running champ.CNA command
... I want to use my own intensity file as the input of champ.CNA function. But I run into the error: > cna=champ.CNA(loadFile = T, file = "intensity.txt", pd=targets, filterXY = F) Run champ.CNA Error in read.table(file, row.names = T, sep = "\t") :   invalid 'row.names' specification   Clearly " ...
champ written 22 months ago by yuping.zhang0 • updated 22 months ago by AST50

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