[BioC] LogFC in Limma

[Gordon K Smyth]

Dear Kevin,

After sending my previous reply, I re-read your email and realized your 
question is probably about a coefficient from lmFit() rather than a 
question about your probe replicates.

It is impossible to give you a definite answer because you haven't told us 
what what your design is or what logFC(1) is measuring, what model you're 
fitting, whether you used contrasts.fit and so on.  Ordinarily, people 
will give enough code to make these things clear.

Since you appear to have at least three columns in your design matrix, it 
seems rather unlikely that logFC(1) could be a simple average of all the 
arrays.

Also, do you have quality weights in your data or blocks in your fit?  In 
these cases, limma will compute weighted averages, which are not the same 
as ordinary averages.

Best wishes
Gordon

> Date: Thu, 23 Oct 2008 13:25:46 -0700 (PDT)
> From: Hai Lin <kevinvol2002 at yahoo.com>
> Subject: [BioC] LogFC in Limma
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <696005.24645.qm at web32404.mail.mud.yahoo.com>
> Content-Type: text/plain
>
> Hello lists,
>
> I am using Bioconductor/Limma package to analyze microRNA arrays.
> I have 7 replicate two-color arrays, 4 probe replicates each array. 
> Follow Limma procedures, I had a list from topTable with LogFC(1) and 
> other columns. In addition, I produced LogFC for each individual arrays 
> from MAlist, the average LogFC(2) were then taken from 7 arrays to 
> compare LogFC(1).
>
> The LogFC(2) is similar to LogFC(1), for example 3.12 vs 3.2, but 
> they're not exactly the same.
>
> My question is that why aren't these two columns of value the same? Did 
> I calculate it mistakenly or something behind this during the Limma 
> procedures?
>
> Could anyone kindly explain it?
>
> Thanks.
>
> Kevin