[BioC] limma anova table?

[Jianping Jin]

Hi Gordon,

Thanks for your reply after a couple of weeks the question was raised! I 
realized that was a silly question to ask a while later after the question 
was posted. I forgot (maybe am not that clear) that lmFit model fit is 
conducted by gene. What I wanted to know was if it is possible to run 
linear model by condition. I wanted to see if a given condition, compared 
to others, has any significant effect on gene expression on a overall 
scale. As you pointed out that there are as many as 55000 genes on a chip, 
plus most gene's expression are unchanged, it won't make any sense to do 
that way.

Thanks again for your comment!

Jianping

--On Tuesday, February 21, 2006 3:06 PM +1100 Gordon K Smyth 
<smyth at wehi.EDU.AU> wrote:

> What anova table do you want exactly?  lmFit() fits a linear model for
> each probe.  Do you want 55,000 anova tables if there are 55,000 probes?
> That doesn't seem very useful to me!
>
> Best wishes
> Gordon
>
>> Date: Tue, 07 Feb 2006 10:34:15 -0500
>> From: Jianping Jin <jjin at email.unc.edu>
>> Subject: [BioC] limma anova table?
>> To: BioConductor_list <bioconductor at stat.math.ethz.ch>
>> Message-ID: <C8B2BE8836479E5ED6585FDF at unc-jpjin.pmbb.med.unc.edu>
>> Content-Type: text/plain; charset=us-ascii; format=flowed
>>
>> Dear limma developer and list:
>>
>> I am wondering if it is possible to extract something like anova table
>> with group Pr. information etc. after "lmFit"?
>>
>> Thanks!
>>
>> 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
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>



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