[BioC] using linear model of limma

[Jenny Drnevich]

Hi Jianping,

>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?

In my experience, quantile normalization does not always remove a batch 
effect. You can test this by using some sort of clustering on the arrays 
using both the raw data and then the RMA values. I like the 'overview' 
function in the made4 package, but I have no idea if it will handle 105 
arrays. If you're going to fit a batch in limma, you should be using 
'duplicateCorrelation', and you can see if the consensus correlation is 
positive; if it's near zero or negative, then your batch effect isn't large 
enough overall to worry about.

Cheers,
Jenny




>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
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives: 
>http://news.gmane.org/gmane.science.biology.informatics.conductor

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu