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 ------------------------------------------------------------------- -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 687 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040105/f0c8c516/attachment.bin

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@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