[BioC] limma topTable question

Cyrus Harmon ch-bioc at bobobeach.com
Mon Apr 4 23:22:09 CEST 2005

Dear bioconductors,

Forgive me if this is in the limma user's guide, but I'd like to be 
able to find the top, say, 100 probe sets in topTable sorted by M, not 
abs(M). I understand that I can do this with sort and resort and then 
filter out the negative ones, but this seems a bit clunky and in a 
sense isn't quite what I've asked, as the top 100 probe sets sorted by 
M after filtering by abs(M) aren't guaranteed to be the same thing, 
unless there are <= 100 probe sets. Yes, I can take the whole resorted 
table and take the top 100 rows, but that seems to be sort of defeating 
the purpose of topTable.

Would it be possible to add another option for M instead of abs(M) for 

Also, the description of what is going on here in the help page is 
rather cryptic. It is only in the discussion of resort.by that the abs 
thing comes up. Furthermore, a better description of what "M" "A", "T", 
"P" and "B" are would be helpful. They are each discussed in the 
context of the Values (for M, t, p and b) and in the Arguments (for A), 
but it would be nice if in the details section, this was recapitulated, 
perhaps with a description of what an A value is, and if the case 
options were spelled out. It seems the only t and p are allowed to be 
lowercase, but it's not clear why.
(Combining my question and my gripe, a sort by "m" that didn't do 
abs(M) would seem useful to me, but perhaps I'm missing something.)



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