[BioC] vsn in limma or marray/arrayMagic

[Gordon K Smyth]

> Date: Tue, 25 Jan 2005 11:30:43 +0100
> From: <A.E.Schiel at lumc.nl>
> Subject: [BioC] vsn in limma or marray/arrayMagic
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID: <8A6C92C9EC1DD74AA66886D8DC3A38CE15545C at mailb.lumc.nl>
> Content-Type: text/plain
>
> Dear all,
> I do have a probably simple question, is running "vsn" in limma (normalizeBetweenArrays) the same
> as running "vsn" in marray or arrayMagic?

Running "vsn" in limma is exactly the same as as running "vsn" in vsn, in fact the vsn package is
simply used as a plug-in.

As far as I know, you can't run vsn from marray.  What do you mean?

If arrayMagic doesn't agree with limma and hence with vsn, then you need to give precise code to
show the discrepancy.  Perhap you have not used the code correctly.

> My Boxplots suggest that there is a difference and I was wondering if someone can give me a hint
> why that might be.
> My particular problem is that I would like to use the fact that my probes are spotted in
> duplicates but not the spacing limma expects. I therefore want to first normalize all my arrays
> (22), then export the data to a text file and resort that file to get the right spacing. If I am
> right I should be able to read such a text file with read.maimages into limma and then continue
> with my analysis. Therefore I would like to know if I need to do my normalization with marray (or
> arrayMagic) or if I can use vsn in limma?

I am puzzled why you would think there is a need to write out to a text file at any stage.

Gordon

> Many thanks in advance,
> Anja