  Paulo Nuin nuin at genedrift.org Mon Oct 31 18:45:54 CET 2011
Hi everyone  I have used Agi4x44Preprocess (script below) to
analyze three mouse (mgug4122a) Agilent microarray sets and I
want to check if the methods I'm using make sense, as the number
of significant p-values I'm getting seems quite high. I'm using
Limma for the significance analysis. the lowest value I'm
getting is 1.09667003222346e-12, while the adjusted p-value
2.43208513046197e-08. If I consider significant p-value below
0.01, I get 9721 significant ones, roughly half of the gene
list. This was for one of the datasets, with 2 (four result
sets) micorarrays, 1 for each treatment. For another similar
dataset, 4 microarrays with 2 samples for each treatment,
results are very similar.  I also tried the approach in this
page http://matticklab.com/index.php?title=Single_channel_analys
is_of_Agilent_microarray_data_with_Limma and the results seem
better (I mean less p-values below 0.01).   I was wondering what
would be the suggested approach and