[BioC] Low Ratio values in LIMMA

[Greg Finak]

Hi, Nataliya.

This is very much dependent on how you normalize your data. It's  
possible to "over normalize" and wipe out most of the variability in  
your data. If you're certain that this isn't the case, then, no,   
Limma doesn't generate shrunken estimates of the expression ratios,  
only t-statistics. The expression ratios presented by limma will  
either be log2, or a data dependent scale if you've used VSN to  
normalize. Feel free to post more information about your  
normalization / preprocessing / experimental design, that would help  
to identify potential reasons, otherwise we're just speculating.

Cheers,


--------------------------------------------
Greg Finak
PhD Candidate
McGill Center For Bioinformatics

W: (514)398-7071 x09317
emai: finak at mcb.mcgill.ca
--------------------------------------------

On 9-Nov-05, at 7:13 PM, Nataliya Yeremenko wrote:

> Hello everybody
>
> After successful importing the data to the LIMMA,
> I followed all steps and finally obtained "topTable".
> (the data were 44K Agilent)
> I'm surprised that my data set doesn't have anything with M-values  
> more
> than 1.5.
> I well understand that it depends on the experiment,
> but is there some condensation of the Ratio during normalization and
> other procedures?
>
> regards
>
> -- 
> Dr. Nataliya Yeremenko
>
> Universiteit van Amsterdam
> Faculty of Science
> IBED/AMB (Aquatische Microbiologie)
> Nieuwe Achtergracht 127
> NL-1018WS Amsterdam
> the Netherlands
>
> tel. + 31 20 5257089
> fax  + 31 20 5257064
>
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