[BioC] can LIMMA deal with count data?

[Bjoern Usadel]

Dear Milena,

probably I am wrong here, since I don't know exactly what kind of data 
you have. But why don't you try Robinson & Smyth's packages for Tag 
abundances.

I was going to point you to his website, but as of today there is a bioc 
package http://www.bioconductor.org/packages/2.3/bioc/html/edgeR.html.
Also check out the papers by Robinson and Smyth.

I guess this might better model your data.

Best Wishes,
björn



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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Björn Usadel, PhD
Max Planck Institute of Molecular Plant Physiology
AG Integrative Carbon Biology
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Tel.: +49 331 5678153
email usadel at mpimp-golm.mpg.de
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