[BioC] External expression data/ MAS5 Signal

Laurent Gautier laurent@cbs.dtu.dk
Mon, 17 Jun 2002 10:02:17 +0200

On Thu, Jun 13, 2002 at 02:04:50PM -0400, Sek Won Kong, M.D. wrote:
> I wondered there's quite a difference in calculated expression values from
> AvgDiff, AvgDiff2, li.wong and rma. Previous I used invariant set normalized
> MAS 5 signal values for analysis. However when I tried to implement the
> quantile normalization and rma, there's big differences in reults ( I mean
> the final results the list of genes ). So I wondered the why, and wanted to
> compare 5 different kinds of expression algorithms.

The 'because' that answers the 'why' is probably linked with the fact that
the methods are fairly different (see their respective description in the
help pages)...
You may want to look at the individual probe sets for the genes for which
the results are very different. (try the function get.PPset)... do not
hesitate to give us feedback about the differences observed.

> And could you let me know how to calculate the PM-only model of Li-Wong in
> affy? li.wong seems like PM-MM model.

In the package, we consider that PMs and MMs probe intensities are used
to compute 'adjusted' probe intensities. In the case of PMs-MMs,
it can be thought of subtracting the noise to the signal.

The parameter 'bg' for express or 'bg.correct' for generateExprSet
(for Plob and Cel.container respectively) let you specify how to
get the 'adjusted' values.
The function 'bg.correct.pmonly' returns only the PMs and can be




Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 85		http://www.cbs.dtu.dk/laurent