User: chelsey.ju

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chelsey.ju0
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Posts by chelsey.ju

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Shinymethyl 850K Array quality control signal cutoffs
... Hello,  I am using the shinymethyl interface to visualize QC of Infinitum MethylationEPICarray data.  I was wondering if there were any known cutoffs used for all of the parameters included in illumina's control probe signals? i.e. bisulfite I, bisulfite II, Negative probe control signal, etc.    ...
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bumphunter output clarification: p values achieved with b=1000: further correction needed?
... Hello,    I have performed the following bumphunter script on my data set: dmrs <- bumphunter(gset, design = designMatrix, cutoff = 0.05, B=1000, type="M") I am wondering if the p values received from this need further corrections, or was that already done with the B=1000? furthermore, I did ...
bumphunter methylation dmr analysis written 2.8 years ago by chelsey.ju0 • updated 2.8 years ago by James W. MacDonald51k
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bumphunter output clarification
... Hello,  I am looking for clarification and explanations for the following output headers of bumphunter DMR analysis:           area cluster indexStart indexEnd L cluster p,value   p,valueArea     Additionally, if a B=1000 permutation cut off ...
minfi bumphunter bioconductor dmr analysis dmr written 2.8 years ago by chelsey.ju0 • updated 2.8 years ago by rafa60

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