[BioC] which genes to choose for being truly differentially expressed from a long list

[James W. MacDonald]

Hi EJ,

On Tuesday, December 03, 2013 10:04:01 AM, EJ [guest] wrote:
>
> Dear All,
> I used LIMMA for a dataset on Human plus 2.0 arrayto get fold change values for differentially expressed genes. I have a long list of 500 some genes with fold changes > 2 from the topTable function. How can I select genes which are most differentially expressed from this list?

You will have to first define what you mean by 'most differentially 
expressed'. If you mean 'largest fold change' then please see 
?topTable, specifically the sort.by argument.

Best,

Jim


>
> Thank you,
> EJ
>
>   -- output of sessionInfo():
>
> R version 3.0.1 (2013-05-16)
> Platform: i386-w64-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252
> [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C
> [5] LC_TIME=English_India.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] limma_3.16.7       affy_1.38.1        Biobase_2.20.1     BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.28.0         BiocInstaller_1.10.3  preprocessCore_1.22.0
> [4] zlibbioc_1.6.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> 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

--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099