[BioC] limma question

[James W. MacDonald]

Sun, Yezhou wrote:
> Hello, Jim,
> 
> Thank you very much for all the suggestions. The problem was solved.
> However I got several new questions:
> 
> 1. what is the exact meaning of -1, 0, 1 in design matrix?

It would take more than an email to answer this question. However, you 
are in luck because Natalie Thorne has posted some really nice slides 
that should help you to figure this out.

http://www.damtp.cam.ac.uk/user/npt22


> 
> 2. I also ran SAM on this data set. There is almost no overlapping
> between top genes picked up by SAM and limma. What could this imply?

Most likely that you have fit a different model in SAM. In my experience 
you don't get wildly different results from SAM and limma, but it might 
not be obvious how to do the same analysis using the two different tools.

> 
> 3. It seems that lmFit requires the number of columns in data set be
> same as the number of arrays in design matrix. So there is no way to put
> probe ID into data set. There are numbers listed in ProbeID field in
> output from topTable(). Are these numbers supposed to be row ID in data
> set?

You *can* put the probe IDs into the data set by setting the row.names() 
of your matrix to be the probe IDs. As an alternative, you can use the 
genelist argument to topTable(). See ?topTable for more information.

> 
> My data set is from GE Codelink platform and has been median centered
> and log2 transformed.

Median centered? You can do much more sophisticated normalizations using 
limma than a simple median centering. Are you sure that this is all you 
need?

> 
> Thanks a lot.
> 
> Yezhou

Jim


-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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