## User: Paul Harrison

Paul Harrison •

**60**- Reputation:
**60**- Status:
- Trusted
- Location:
- Twitter:
- @paulfharrison
- Last seen:
- 10 months, 2 weeks ago
- Joined:
- 5 years, 8 months ago
- Email:
- p************@monash.edu

#### Posts by Paul Harrison

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... 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 13 months ago by
Paul Harrison •

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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 15 months ago by
Paul Harrison •

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... 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 ...

written 2.1 years ago by
Paul Harrison •

**60**• updated 2.1 years ago by Gordon Smyth ♦**35k**0

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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 4.4 years ago by
Paul Harrison •

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... 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 ...

written 4.4 years ago by
Paul Harrison •

**60**• updated 4.4 years ago by Gordon Smyth ♦**35k**0

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... 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 5.7 years ago by
Paul Harrison •

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... 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 5.7 years ago by
Paul Harrison •

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... 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 5.7 years ago by
Paul Harrison •

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... 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 ...

written 5.7 years ago by
Paul Harrison •

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