14.0 years ago by
On 11/9/05 7:13 PM, "Nataliya Yeremenko" <eremenko at="" science.uva.nl="">
> 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
> 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?
If I understand your original question, you are asking about M-values
reported by topTable? These M-values are the log2 fold-change
with the contrast associated with that coefficient. In other words,
are doing a two-group comparison in limma (as a simple example), the
represents the average log2 fold-change between the groups. If you
getting large M-values, then you do not have large differences between
Of course, normalization can have a significant effect on the fold-
that you see in topTable, but another likely explanation,
aside, is that there are not large differences between groups.
I may have misunderstood your question, but I'm not sure that
is the culprit here. And I think that most would advocate doing
normalization based on biologic understanding of the experiment and
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
list (not that you were going to do so).
Hope this helps,