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
> x Fax: (919)843-3103 x
> x E-mail: jjin at email.unc.edu x
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
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
>> x Fax: (919)843-3103 x
>> x E-mail: jjin at email.unc.edu x
>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>
>
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
