edgeR: confusing BCV plot
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@gordon-smyth
Last seen 31 minutes ago
WEHI, Melbourne, Australia
> Date: Wed, 12 Sep 2012 13:43:25 +0000 > From: Natasha Sahgal <nsahgal at="" well.ox.ac.uk=""> > To: "James W. MacDonald" <jmacdon at="" uw.edu=""> > Cc: "'bioconductor at r-project.org'" <bioconductor at="" r-project.org=""> > Subject: Re: [BioC] edgeR: confusing BCV plot > > Dear Jim, > > Regarding the BCV plots, what I did not understand was the strange profile (at least strange to me), and the low coefficients of BV. > Based on some figures from the user guide, it appeared to be very different - an increase towards the higher logCPM. > 1) I'm not sure how to interpret these and if it is a good thing or not? (perhaps I have misunderstood the concept of the BCV) Suggests to me that there is something unusual about your data. Especially the J shape at very low counts, which I have not seen before for RNA-seq data. > 2) How does this affect the differential expression, if at all? Genes that have larger estimated dispersions are less likely to be judged to be differentially expressed. Gordon > Re the filtering, for some reason I was under the impression increasing the counts per million would reduce (if not remove) zero counts in all samples. I agree with what you say about half the samples being unconstrained. > > I had 3 filters here, just to see what the difference would be. I still need to figure out the best or optimal one to use. > > > Many Thanks and Best Wishes, > Natasha > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
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