[BioC] extract lmFit results?

[Jianping Jin]

Many thanks for your explanation!
have a nice weekend!
JP-

--On Friday, February 17, 2006 3:11 PM -0500 "James W. MacDonald" 
<jmacdon at med.umich.edu> wrote:

> Hi Jianping,
>
> Jianping Jin wrote:
>> Thanks James!
>>
>> Please forgive my ignorance if I am wrong. I knew "fit$coefficients"
>> stuff.  That just give me "coefficients". Is that "b" in y = a + bx? It
>> must be  more complicated than that I guess. In my case I just used
>> default "design"  in fitting as below:
>
> Well, that formula is conventionally used to describe a linear regression
> where there is some concept of slope. We are fitting an ANOVA model, and
> since there is no ordering of the factor levels, there is no concept of
> slope. A more conventional formula for ANOVA (without the subscripts)
> would be something like
>
> y = a + b + error
>
> The coefficients would correspond to 'a' and 'b', which depending on the
> design matrix can mean different things.
>
>>
>> fitR <- lmFit(RG$R, ndups=2, spacing=722, correlation=0.5205939)
>
> Hmmm. I haven't done any cDNA work in years, but I don't think that looks
> right. If I am not mistaken, what you are doing is fitting a one-sample
> t-test on just the cy5 (or is cy3 red? I can never remember) values which
> is usually not what you want. The convention is to fit a one-sample
> t-test on the log ratios, which then tests to see if the average log
> ratio is different from zero (which corresponds to testing if the average
> fold change is different from one).
>
> The model here would be
>
> y = a + error
>
>
>>
>> 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?
>
> If by 'y' values you mean the fitted values, you would get those from the
> fit$coefficients, which in your case should just be a vector, one value
> per gene.
>
> HTH,
>
> Jim
>
>
>
>>
>> Thanks again!
>>
>> Jianping
>>
>> --On Friday, February 17, 2006 1:27 PM -0500 "James W. MacDonald"
>> <jmacdon at med.umich.edu> wrote:
>>
>>
>>> Jianping Jin wrote:
>>>
>>>> Dear list,
>>>>
>>>> Could anyone point me out how to extract the results from lmFit? The
>>>> on-line document said "the probe-wise fitted model results are stored
>>>> in a  compact form". What I wanted to get is ALL data values after
>>>> linear model  normalization instead of going through all limma
>>>> processes.
>>>
>>> The results are output in a named list. As with all named lists, you can
>>> extract the names using names(listname). If, for example, your lmFit()
>>> output is called 'fit', you can get information in several ways:
>>>
>>> names(fit) ## gives names
>>> fit ## outputs first 10 or so values in each list component
>>> fit$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
>>
>> _______________________________________________
>> 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