[BioC] Limma package and minimal number of genes

Ryan rct at thompsonclan.org
Wed Jun 11 06:09:47 CEST 2014

Ah, yes, re-reading the original question, this is the correct answer. 
Filtering genes by biological annotation (e.g. just TFs) should be done 
after running limma.

On Tue Jun 10 19:47:59 2014, Paul Geeleher wrote:
> 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.
> Paul
> 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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