[BioC] SAM vs. Limma

[Fangxin Hong]

Well, first SAM is only used to compare two samples (one comparison at a
time) and identify differentially genes, while limma can make more than
one comparison at a time through modelling fitting, e.g., 3 pairwise
comparison out of 3 samples. Second, limma is also able to perform other
analysis beside identifying differentially expressed genes, like test the
interaction terms in expression profiles, study the effect of a particular
factor in gene expression. And the bottom line is: SAM is non-parametric
which doesn't have any assumption whie limma does assume a linear model
for the expressin.

That is what came to my mind immediately, but there should be more.
Hopefully this helps.

Fangxin


> I would like to know why some of you bioconductorians are using Limma and
> some are using Sam. I find some quite convinient and the theory seems
> straightforward in a statistical sense. Please let me know what your
> reasons are for using one of these two approaches.
> Cheers
>
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-- 
Fangxin Hong, Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu