[BioC] (no subject)

[w.huber at dkfz-heidelberg.de]

Hi Anna,

it does not hurt to read the help pages. The function mva.pairs expects a
matrix. A call like the following should work:

mva.pairs(exprs(eset), log.it=FALSE)

(Oddly enough, the default of this function is to log the data.) However,
if you have many (n) chips, rather than looking at all n*(n-1)/2 pairs of
chips, it might be more illuminating to do something like:

A = rowMeans(exprs(eset))
for (i in 1:nrchips) {
  M = exprs(eset)[,i] - A
  plot(A, M, pch=".")
}

Best,
  Wolfgang

-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/mga/whuber
-------------------------------------











On Thu, 14 Aug 2003, Anna Gustafsson wrote:

> Dear all,
>
> Unfortunately - more questions:
> I wonder how to use mva.pairs to plot 2 replicate slides from an "eset" object of background corrected, normalized, pm corrected and summarized data (i.e rma output).
>
> I can only find a vignette describing plots from only normalized, non summarized (16 individual expression measures / gene plotted) and I do not understand how to transfer that information to work for my data in the "eset" format..... :(
>
> With hopes on help!
>
> // Anna   :o)
>
> *******************************************************************************************
> Anna Gustafsson
>
> Royal Institute of Technology
> AlbaNova University Center
> Stockholm Center for Physics, Astronomy and Biotechnology
> Department of Molecular Biotechnology
> 106 91 Stockholm, Sweden
>
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