User: dalerr

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dalerr0
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Posts by dalerr

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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 2.8 years ago by dalerr0 • updated 2.8 years ago by Gordon Smyth39k
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Comment: C: Differential Pol2 pausing analysis
... OK, I'll give that a shot. Thanks very much for your help! ...
written 2.8 years 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 2.8 years 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 2.8 years 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 2.8 years ago by dalerr0 • updated 2.8 years ago by Aaron Lun25k

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