[BioC] LogFC query in Limma

[Steve Lianoglou]

Hi,

On Thu, Jan 31, 2013 at 2:54 PM, Roopa Subbaiaih <rss115 at case.edu> wrote:
> Hi All,
>
> Thanks for the reply, I could pull out the the whole information for
> differentially expressed genes. The criteria used was adjust="fdr", p=0.05.
> I came up with ~ 20,000 genes to be differentially expressed.

Hmm ... surely 20k cannot be correct?

> Since I wanted to analyze these genes for deregulated pathways I had to
> come up with fold change values for further analysis.
>
> I assume that for each gene FC= FCmean(test)-FCmean(blank). LogFC is log2
> of FC values.
>
> When I convert the FC values (test/blank) to foldchanges using IF function
> I get lesser number of genes to be deregulated. The criteria was =>2
> foldchanges and =<-2 fold changes.

I'm missing previous context to this email, so -- not sure what the
"IF function" is, but if you're using limma, the log2fold changes are
reported for you in the logFC column that is returned from
`topTable(...)`

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact