[BioC] Limma package and minimal number of genes

Paul Geeleher paulgeeleher at gmail.com
Wed Jun 11 04:47:59 CEST 2014

Limma borrows information across all genes to better estimate variance
for each gene, so your results should in theory be more accurate if
you run the analysis for all genes on your arrays and export the
p-values for the set of genes in which you are interested at the end
of the analysis.


On Tue, Jun 10, 2014 at 3:34 AM, Bas van Gestel
<shc.van.gestel at gmail.com> wrote:
> Dear all,
> Currently, I'm comparing the gene expression of three cell types to
> identify differentially expressed genes. For this purpose, the limma
> package seems ideal. However, for one of the analyses, I would like to
> focus only on the transcription factors of the cell types. This implies
> that I only consider about 990 genes. Is this enough to perform an analysis
> with limma, or does it require a larger number of genes at minimum to give
> reliable results?
> Kind regards,
> Bas van Gestel
>         [[alternative HTML version deleted]]
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Dr. Paul Geeleher, PhD
Section of Hematology-Oncology
Department of Medicine
The University of Chicago
900 E. 57th St.,
KCBD, Room 7144
Chicago, IL 60637

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