[BioC] information about Li-Wong

[James MacDonald]

Note that the express function is deprecated. You now should use
expresso. For detailed information, please see the builtinMethods.pdf
that comes with the affy package, or the expresso and liwong help
pages.

In short, to replicate the Li and Wong method, you would do something
like this:

eset <- expresso(abatch, bgcorrect.method="none",
normalize.method="invariantset", 
		pmcorrect.method="pmonly", summary.method="liwong")

This will give you results similar to the PM-only Li and Wong model. If
you want PM-MM, you should use pmcorrect.method="subtractmm".

Also note that you really need maybe 10+ chips to use this method. With
fewer chips you will start running into convergence problems for a lot
of the genes, and you will get bunches of warnings.

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Bettina Harr <harr at uchicago.edu> 01/05/04 09:47AM >>>
Hi list,

I would like to get expression values according to the Li-Wong method.

I found this function

liwong <- express(affybatch.example, summary.stat=li.wong)


and I wonder whether somebody could tell me what the function actually

uses for background correction, normalization and pm.correct??

Thanks

Tina

-------------------------------------------------------------------
Bettina Harr
Abteilung fuer Evolutionsgenetik
Institut fuer Genetik
Universitaet zu Koeln
Weyertal 121
50931 Koeln - Germany
Tel: ++49 221 470 6912
Fax: ++49 221 470 5975