
Hi Gordon,
 
Thanks for your prompt reply. I have looked at the sections you mentioned in your email. What I am looking for is more of standard statistcis for individual factors even before doing a contrast. 
If I go with the linear model fit (the first fit before the contrast matrix), is there a way to pull the mean, sd, cv, variance etc. out of the fitted object for each factor? 
I am looking at a large gene expression study using afymetrix plus 2 chips. I have 4 factors (blood compartment, gender, time, subject) and I want to look at the variability of each of the factors on the basis of the entire chip: e.g. by boxplots of cvs of all probesets for each factor. Can I make use of limma to get this information?
 
Any suggestions would be greatly appreciated.
 
Thanks,
Som.
 

> Date: Tue, 20 Dec 2011 09:39:24 +1100
> From: smyth@wehi.EDU.AU
> To: genome1976@hotmail.com
> CC: bioconductor@r-project.org
> Subject: Re: LIMMA: extracting simple stats for factors and levels from lmfit
> 
> Please see Sections 10.1 and 10.2 of the limma User's Guide. You can 
> compute the statistics you want from the provided components.
> 
> Gordon
> 
> On Mon, 19 Dec 2011, somnath bandyopadhyay wrote:
> 
> > Is there a way to extract simple stats like sd, cv, mean, variance for each probeset from lmfit objects? Is there any other way to extract the info for a large experiment with multiple factors and levels? Any suggestions would be greatly appreciated.
> > Thanks,
> > Som.
> 
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