User: Paul Harrison

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Posts by Paul Harrison

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Answer: A: Bootstrap confidence intervals on RNA-seq expression from Kallisto
... Since RNA-seq is count based, in an RNA-seq analysis at the gene level the noise in individual counts for genes can be assumed to be Poisson (variance equal to the mean). This is an estimate of "technical variation", but does not include "biological varation". This would be the equivalent of the Kal ...
written 7 weeks ago by Paul Harrison60
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Comment: C: Limma-voom vs limma-trend
... If you examine the documentation to `contrasts.fit`, there is a warning that using weights with a non-orthogonal design matrix uses an approximation. Since voom uses weights on inidividual observations, and limma-trend does not, this could be an advantage to using limma-trend. ...
written 4 months ago by Paul Harrison60
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In limma's barcode plot, why are the cutoffs for the pale red and blue bands +/-sqrt(2)?
... limma's barcodeplot function by default draws a pale red rectangle for statistics greater than sqrt(2) and a pale blue rectangle for statistics less than -sqrt(2). What is the reasoning is behind this choice? Is the expectation that statistics follows a standard normal distribution for genes that a ...
limma barcodeplot written 14 months ago by Paul Harrison60 • updated 14 months ago by Gordon Smyth32k
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Comment: C: Behaviour of weights in limma
... On Thu, Jun 5, 2014 at 10:04 AM, Gordon K Smyth wrote: > Dear Paul, > >> Date: Wed, 4 Jun 2014 17:30:59 +1000 >> From: Paul Harrison >> To: Bioconductor mailing list >> Subject: [BioC] Behaviour of weights in limma >> >> Hello, >> >> I have so ...
written 3.4 years ago by Paul Harrison60
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Behaviour of weights in limma
... Hello, I have some data from a variant of RNA-seq which I am hoping do some moderated t-test differential testing on with limma. In this data, many of the reads have sequenced through into the poly(A) tail, and we believe this gives us information about changes in poly(A) tail length. For each gen ...
limma written 3.5 years ago by Paul Harrison60 • updated 3.5 years ago by Gordon Smyth32k
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Comment: C: Log transformation and left censoring
... On Mon, Feb 4, 2013 at 7:56 PM, Wolfgang Huber wrote: > > Hi Paul > > the model (in the "parametric" case) is > > var(X) = a * E(X) + b * E(X)^2 > > with some a,b>0. And you are right that var(X)=0 <=> E(X)=0 > but since the support of X is positive, the onl ...
written 4.8 years ago by Paul Harrison60
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Comment: C: Log transformation and left censoring
... On Tue, Feb 5, 2013 at 11:23 AM, Gordon K Smyth wrote: > Dear Paul, > > The transformation that you propose is the same transformation that is done > by predFC(y) in the edgeR package, or by cpm(y,log=TRUE) in the > developmental version of the edgeR package. The argument prior.coun ...
written 4.8 years ago by Paul Harrison60
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Answer: A: Log transformation and left censoring
... On Sun, Feb 3, 2013 at 10:24 PM, Wolfgang Huber wrote: > > Hi Paul > > given your description, one possibility to explore might be a variance > stabilising transformation. > > E.g. DESeq provides one that smoothly interpolates between the square-root > function for low count ...
written 4.8 years ago by Paul Harrison60
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Log transformation and left censoring
... Hello, We have been using voom and limma for some time now, and while we're fairly happy with it, it seems to produce significance levels that are on the conservative side. We also use edgeR to produce more optimistic results, but don't entirely trust the significance levels that it reports. I am l ...
limma safe edger written 4.8 years ago by Paul Harrison60

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