[BioC] Limma package and minimal number of genes

[Ryan]

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]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>