Hi Wendy,

Depending on your number of cell types, you can try the SpeCond package for
your analysis. It allows to detect condition-specific gene expression, in
your case cell-type specific gene expression.
Let me know if you have any questions about it.
Best,
Florence

2011/4/10 Wendy Qiao <wendy2.qiao@gmail.com>

> Hi all,
>
> I am comparing a number of cell types, and am wanting to find the signature
> genes of each cell type. I used the limma package to do this. The signature
> genes of a given cell type are found by the fold different between the
> given
> cell type and grand mean of all the cell types, as well as the BH-adjusted
> p-values. I want to add another condition to test the consistency of
> expression levels of the selected genes for each cell type. I can do this
> by
> looking at the standard deviations of gene expressions between replicates.
> I
> am just wondering if there is any function in limma or other BioConductor
> package to do this.
>
> Thank you in advance,
>
> Wendy
>
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>
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-- 
----------------------------------------
Florence Cavalli
PhD student, Luscombe group
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
CB10 1SD
Cambridge
UK
email: florence@ebi.ac.uk

Global poverty project | Cambridge
http://www.globalpovertyproject.com/

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