[BioC] ttest or fold change

Crispin Miller CMiller at PICR.man.ac.uk
Tue Dec 16 19:18:51 MET 2003

Hi Jim,

> You only have to adjust for the multiple comparisons you have made,
> not those you could have made.

I take your point, but I'm still concerned that a hypothesis I would
have accepted six months ago is now something I'd reject. If nothing
else, because I have to explain why :-) I think there is a wider issue
about the logical decisions that need to be made about how one groups
the data in order to apply  a correction... Another example:

Scientist A is interested by what is up-regulated by his transcription
factor. He does a real-time experiment with replicates and finds a gene
with significant induction. Scientist B is also interested in the same
transcription factor. She does a similar real-time experiment on a
different gene (but with the same transcription factor). Does she do
multiple testing correction to take into account the previous work by A?

(I think this is very similar to the new-v-old chips question, but with
different numbers).

I did a quick search on the web and this sort of thing appears to have
been discussed quite a lot before - e.g. 'To Bonferroni or not to
Bonferroni...' Cabin and Mitchell (2000), which is cited a fair number
of times by articles in Ecology journals...

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