[BioC] using linear model of limma

[Jianping Jin]

Dear list,

This is a follow-up info to my first email (see below). I tried to use 
lmFit on my raw data, data at exprs which is a read.affybatch object. I 
realized that there was no way for me to retrieve the linear model fitted 
resulting values for next data procession as the results are stored in a 
compact form as stated in the on-line help document.

It looks like that the easier way to handle the chip batch effect for my 
data is to include "batch" as a factor in the fit model and let limma do 
the further procession.

So the usual processes are reading .CEL files in, preprocessing data with 
RMA/GCRMA, fitting data with linear model and then using eBayes. I have 
questions here, please forgive me as a none statistician, if the quantile 
normalization in RMA would do any harm than good to the data when a batch 
effect exists? What else does lmFit do if RMA has already removed the batch 
effect?

Please help me out for this confusion.

thanks!

Jianping

--On Wednesday, November 15, 2006 11:50 AM -0500 Jianping Jin 
<jjin at email.unc.edu> wrote:

>
> Dear list:
>
> A batch effect was observed in 16 out of 105 hgU133_plus2 arrays based on
> NUSE plot. I know SAM, like limma, is able to handle this kind of thing
> with setting block. But I am not sure if that is appropriate way for this
> unintentional situation.
>
> I would try to use the lmFit function of limma with batch as a factor to
> remove the batch effect. Then use the resulting data values for other
> software applications, for example SAM. Here come my questions:
> 1. Should I apply the raw data, data at exprs, instead of eset at exprs for
> running lmFit?
> 2. If that is a right way, how can I extract the lmFit normalized data
> for next RMA or GCRMA?
>
> Please point it out if I am confused with something! I will appreciate
> your help!
>
> Jianping
>
> ##################################
> Jianping Jin Ph.D.
> Bioinformatics scientist
> Center for Bioinformatics
> Room 3133 Bioinformatics building
> CB# 7104
> University of Chapel Hill
> Chapel Hill, NC 27599
> Phone: (919)843-6105
> FAX:   (919)843-3103
> E-Mail: jjin at email.unc.edu



##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu