[BioC] Low Ratio values in LIMMA

[Sean Davis]

On 11/9/05 7:13 PM, "Nataliya Yeremenko" <eremenko at science.uva.nl> 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

Nataliya,

If I understand your original question, you are asking about M-values as
reported by topTable?  These M-values are the log2 fold-change associated
with the contrast associated with that coefficient.  In other words, if you
are doing a two-group comparison in limma (as a simple example), the M-value
represents the average log2 fold-change between the groups.  If you are not
getting large M-values, then you do not have large differences between your
groups.  

Of course, normalization can have a significant effect on the fold-changes
that you see in topTable, but another likely explanation, normalization
aside, is that there are not large differences between groups.

I may have misunderstood your question, but I'm not sure that normalization
is the culprit here.  And I think that most would advocate doing
normalization based on biologic understanding of the experiment and global
characteristics of the data and not the resulting fold-changes or
significance; it really probably isn't a good idea to do multiple
normalizations looking for the one that gives the best fold-change or gene
list (not that you were going to do so).

Hope this helps,
Sean