[BioC] extract lmFit results?

[James W. MacDonald]

Jianping Jin wrote:
> Dear list,
> 
> Could anyone point me out how to extract the results from lmFit? The 
> on-line document said "the probe-wise fitted model results are stored in a 
> compact form". What I wanted to get is ALL data values after linear model 
> normalization instead of going through all limma processes.

The results are output in a named list. As with all named lists, you can 
extract the names using names(listname). If, for example, your lmFit() 
output is called 'fit', you can get information in several ways:

names(fit) ## gives names
fit ## outputs first 10 or so values in each list component
fit$coefficients ##extract coefficients
fit$p.value ## p-values
etc.

See ?list, ?"[["  for more information.

HTH,

Jim


> 
> Thanks in advance!
> 
> Jianping
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
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