User: kuckunniwid

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Posts by kuckunniwid

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Comment: C: Internal bug of DMR-Seq?
... Thanks a lot! Will reinstall and check! ...
written 8 weeks ago by kuckunniwid0
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Comment: C: Internal bug of DMR-Seq?
... Dear Keegan, thanks a lot for the answer. Once I'll receive the permission I will send it to you. I faced another error: ...Chromosome chrUn_KI270333v1: Error in (function (classes, fdef, mtable)  :   unable to find an inherited method for function ‘rowSums2’ for signature ‘"DelayedArray"’ Other ...
written 9 weeks ago by kuckunniwid0
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Comment: C: Internal bug of DMR-Seq?
... I think that the error is random and happens due to some incorrect permutations. So there is no "safe" settings - sometimes I lucky to not to get the error, sometimes I am not. And of course it takes a lot of time, each computation, so it is really nervous - waiting for the end of computations while ...
written 9 weeks ago by kuckunniwid0
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Comment: C: Internal bug of DMR-Seq?
... The code that leads to error is: library(data.table) library(gplots) files <- list.files(pattern = "\\.cov.gz$") readBismarkFile <- function(fileName) {   bismarkCoverage = fread(paste('zcat', fileName) ,stringsAsFactors = F)   bismarkCoverage = bismarkCoverage[,-4]   colnames(bismarkCoverag ...
written 9 weeks ago by kuckunniwid0
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Comment: C: Internal bug of DMR-Seq?
... Hi keegan, thanks for the fast reply! I have troubles even with the first line - somehow my DmrSeq worked without the package BiocManager. Installed it, the output is  > BiocManager::valid() * sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubu ...
written 9 weeks ago by kuckunniwid0
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Internal bug of DMR-Seq?
... Working with DMR-seq I get the following error message from time to time: Detecting candidate regions with coefficient larger than 0.05 in magnitude. ...Chromosome chr1: Smoothed (0.89 min). 335 regions scored (1.64 min).  ...Chromosome chr10: Smoothed (0.74 min). 117 regions scored (0.38 min).  .. ...
dmrseq written 9 weeks ago by kuckunniwid0 • updated 5 weeks ago by keegan50

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