[BioC] can LIMMA deal with count data?

[Mark Robinson]

Hi Milena.

Short answer is no, limma cannot model count data.

Gordon and I have developed a method that will operate on count data  
(such as nextgen sequencing) by doing moderation on the dispersion  
parameter of a negative binomial model:
http://www.ncbi.nlm.nih.gov/pubmed/17881408

The R package will come out with Bioconductor 2.3, due for release on  
October 20th.  You can get an advance copy at:
http://www.bioconductor.org/packages/2.3/bioc/html/edgeR.html

There are other groups working on similar moderated approaches but I  
haven't seen any results yet.

Its a brand new package, so I'm keen to get some feedback.

There is also a facility in the package for Poisson data.

Cheers,
Mark



On 26/09/2008, at 3:39 PM, Milena Gongora wrote:

> Hello limma users.
>
> Can LIMMA fit a linear model to a Poisson distribution?
>
> My dataset is equivalent to an array but instead of intensities the  
> genes have counts (it is sequence data). I would like to perform an  
> eBayes() kind of analysis. However, is seems that this data has the  
> attributes of a poisson distribution and (please correct me if I am  
> wrong) fitting the linear model using lmFit() would not be suitable...
>
> So I wonder if there is another function that can fit a gene-wise  
> linear model for this type of error distribution? sort of like  
> glm(family=poisson) but for the whole array? And after this, would I  
> be able to use eBayes()?
>
> I appreciate your insight.
>
> Thanks,
> Milena
>
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------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
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