[BioC] straight t vs. bonferroni vs. all the new stuff.

[Matthew Lyon]

Esteemed List:

i need an alpha value for a t-test with about n=450,000 and a
1) df of 2
2) df of 4

this is microarray data. i've been told bonferroni is too conservative for 
microarrays, hence interesting approaches like multtest, the q-value 
permuted one, etc...

can anyone who deals in this area extensively (say, expression data) give me 
a ballpark value for t- or alpha- that's typically giving good 'oh man this 
is significantly different!' results ? i've got my own hunches but would 
like some blinded numbers tossed at me too.

Thank You,

Matthew Lyon        UC  Riverside                    lab (951) 827-4736
Ph.D. Student        B O T A N Y                new c.p. (951) 941-5554
                   Citrus Genomics                    apt (951) 328-9930
http: // int - citrusgenomics . org /           messengers: ptrifoliata
mattlyon at mattlyon.com ptrifoliata at hotmail.com mlyon003 at student.ucr.edu