[BioC] package/function for median center & unit variance

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Jul 11 15:25:05 CEST 2011

Hi Guido,

On Mon, Jul 11, 2011 at 9:17 AM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
> Dear list,
> After (RMA) normalization I would like to post-process my array data for downstream analyses by means of median centering and/or unit variance normalization.
> Does anyone know a library that contains these functions?
> Using available functions would minimize the chance on errors due my limited R coding skills... ;) I had a look at the library Genefilter but it doesn't contain these functions.

The base `scale` function will get yo close to where you want to be.
It works on a matrix, so you'll have to get your `exprs` matrix out of
your RMA normalized data.

By default, `scale` actually does mean-centering and then divides the
columns by their std.dev. The help page for `scale` will also point
you to `sweep` which has an example of how to median center the
columns of a matrix.



Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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