[BioC] extract lmFit results?

[Jianping Jin]

Thanks James!

Please forgive my ignorance if I am wrong. I knew "fit$coefficients" stuff. 
That just give me "coefficients". Is that "b" in y = a + bx? It must be 
more complicated than that I guess. In my case I just used default "design" 
in fitting as below:

fitR <- lmFit(RG$R, ndups=2, spacing=722, correlation=0.5205939)

What if I am interested in getting all "y" values for each gene in each 
chip after lmFit fitting? Do I need to calculate them out following some 
formula? Or I can extract them from somewhere within the limma package?

Thanks again!

Jianping

--On Friday, February 17, 2006 1:27 PM -0500 "James W. MacDonald" 
<jmacdon at med.umich.edu> wrote:

> 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



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