[BioC] "romer"ing and "roast"ing around gene sets

[Robert M. Flight]

Hi All,

I am having trouble with the distinction between the functions "roast"
and "romer" in the limma package. From the publication describing
"roast" (http://dx.doi.org/10.1093/bioinformatics/btq401), it seems
that it tests a particular gene set for differential expression,
whereas "romer" tests a battery of sets to find those that are
differentially expressed compared to the rest?

I am really having trouble discerning the true difference between
these two, and how they compare to GSEA. I always thoght that the
primary purpose of GSEA was to determine those gene sets that are
significantly associated with a phenotypic comparison, i.e. those gene
sets showing differential expression.

If any one can help me clear this up, that would be great, because as
of now I am thoroughly confused. To me, if I have a dataset, and I
want to know which gene sets (from say MSigDB) are differentially
expressed, then it sounds like I would use "roast", but the way it is
described in the publication (and the help in limma), this isn't what
I would do, but rather I should use "romer", and see if any of the
sets show differential expression compared to the rest in the
database.

Color me confused,

-Robert

Robert M. Flight, Ph.D.
Bioinformatics and Biomedical Computing Laboratory
University of Louisville
Louisville, KY

PH 502-852-0467
EM robert.flight at louisville.edu
EM rflight79 at gmail.com

Williams and Holland's Law:
       If enough data is collected, anything may be proven by
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