User: parker

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parker0
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Posts by parker

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bsseq - dmrFinder error
... Hello, I have previously used the bsseq package to get a list of dmrs successfully. However, now I have encountered an error when I run the dmrFinder - please see below: Any help is much appreciated. Thank you! Hannah > data.tstat An object of type 'BSseqTstat' with 3142216 methylation l ...
bsmooth bsseq r package dmrfinder written 2.4 years ago by parker0
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Answer: A: BSseq package for Targeted DNA bisulfite sequencing for DMR analysis
... Thank you very much for your answer - I have looked into this package and it looks more appropriate for targeted analysis. I am following your protocol and I want to try and create the BSraw object with the Bismark output files. However, when I run readBismark(files, colData) I get an error:  Erro ...
written 4.7 years ago by parker0
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BSseq package for Targeted DNA bisulfite sequencing for DMR analysis
... Dear All,  I am analysing data produced from Zymo's Targeted Bisulfite sequencing approach which uses a Fluidigm's array to simultaneously amplify 48 samples using 48 specific genetic loci. I have a heterogenous mix of samples but have started comparing cancers with normal tissue. I am having some ...
methylation dmr analysis written 4.7 years ago by parker0
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Answer: A: Error using Bsmooth.tstat due to NAs
... I am also having the same problem - but when I get the information on the smoothed data:  summary(getMeth(bsseq.data.smoothed)) I see that there are quite a few NAs ~700 for most of my samples. I don't know whether this is because I did a targeted approach and many of the CpGs were not targeted. I ...
written 4.8 years ago by parker0

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