[BioC] extract lmFit results?

James W. MacDonald jmacdon at med.umich.edu
Fri Feb 17 19:27:18 CET 2006


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
> 
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> x Jianping Jin Ph.D.            x
> x Bioinformatics scientist      x
> x Center for bioinformatics     x
> x 3133 Bioinformatics Building  x
> x CB# 7104                      x
> x University of North Carolina  x
> x Chapel Hill, NC 27599         x
> x Tel: (919)843-6105            x
> x Fax: (919)843-3103            x
> x E-mail: jjin at email.unc.edu    x
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


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



More information about the Bioconductor mailing list