User: dalerr

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dalerr0
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Posts by dalerr

<prev • 5 results • page 1 of 1 • next >
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edgeR minor bug in normalizeChIPtoInput
... Very minor issue; I noticed that some return calls in normalizeChIPtoInput.R are missing list() at https://github.com/Bioconductor-mirror/edgeR/blob/master/R/normalizeChIPtoInput.R#L24 which will give an error Error in return(p = rep(0, 1), scaling.factor = 0, prop.enriched = 1) : multi-argument ...
edger written 9 months ago by dalerr0 • updated 9 months ago by Gordon Smyth32k
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Comment: C: Differential Pol2 pausing analysis
... OK, I'll give that a shot. Thanks very much for your help! ...
written 9 months ago by dalerr0
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Comment: C: Differential Pol2 pausing analysis
... Hmm. Let's make the simplifying assumption that coverage is uniform across TSS and across gene body. Practically speaking, how would I incorporate region size normalization into edgeR? Would this be an offset? ...
written 9 months ago by dalerr0
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Comment: C: Differential Pol2 pausing analysis
... Thank you so much for this. Way more elegant than the path I was on and the results are now looking quite good. Follow-up question: I hope to do some downstream filtering on which genes were paused in the control. Based on your arguments above on ignoring input and sample as blocking factor, would ...
written 9 months ago by dalerr0
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Differential Pol2 pausing analysis
... I am trying to use edgeR for differential Pol2 pausing analysis but I am unsure if I'm on the right track. "Pol2 pausing index" is the ratio of Pol2 ChIP in a gene's promoter vs downstream. I'd like to identify how this changes between control and treatment. I'm unable to find a published method th ...
chipseq edger csaw differential binding analysis written 9 months ago by dalerr0 • updated 9 months ago by Aaron Lun17k

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