[BioC] (no subject)

[James MacDonald]

Wenqiong,

limma is quite adept at determining what you are using and taking the
correct actions. For instance, the help for lmFit has this to say about
what sort of data object you can pass to lmFit:

object: object of class 'numeric', 'matrix', 'MAList', 'marrayNorm'
          or 'exprSet' containing log-ratios or log-values of
          expression for a series of microarrays

So you should be able to pass your data after coercing to a matrix.

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Wenqiong Chen" <wenchen at diversa.com> 02/26/04 08:01PM >>>
Hi, 
I have a limma question. I have some proteomic data which I would like
to
analyze using limma and compare the results to that using LPE. What I
have
is a couple of data frames with genes in rows and experiments in
columns,
similar to Affymetrix data like single-channel design. How can I plug
in
these data into available functions in limma to do the analysis. Maybe
I
have missed something but looks like limma only takes eset from Affy
data?
Can I directly replace eset with my data.frame in when calling lmFit
function?
Thanks,
wenqiong

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