Entering edit mode
kerick@molgen.mpg.de
▴
10
@kerickmolgenmpgde-1320
Last seen 9.6 years ago
Dear all,
to the best of my knowledge these questions haven't been posed so far;
I
apologize if I didn't dig deep enough.
I am seeking advice on which option to choose from the decideTests
function in
limma. Since the methods nestedF, heirarchical, global and separate
(all using
fdr adjustment) give pretty different numbers of genes being
classified as
significant I wonder which choice is statistically speaking the most
stringend
and which is the least stringend. Any idea how to line up all choices
with
regard to increasing stringency? nestedF < heirachical < global <
separate ..maybe?
practical questions:
We performed an experiment which tries to answer seven questions(~ 7
contrasts).
I chose the nestedF option to get a fair amount of "differentially
regulated"
genes for each contrast to then perform fisher.test analysis on
geneontology
groups for each contrast separately.
Then I chose the heirarchical option to have a closer look at the
genes one by
one for each contrast at hand.
Any doubts concerning this strategy?
I appreciate any comment,
Best regards,
Martin