I installed the affy_1.1.3.zip package and I tried the Laurent expresso patch of Jan 8. I get the following error: peter3.eset <- expresso(peter3,normalize.method=FALSE, bgcorrect.method="mas", pmcorrect.method="mas", summary.method="mas") background correction: mas normalization: FALSE PM/MM correction : mas expression values: mas background correcting...done. normalizing...Error in pmatch(x, table, duplicates.ok) : argument is not of mode character As a sanity check, the following rma call works fine on my data set: peter3.eset <- rma(peter3) Thanks, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Environmental Health, Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 ********************************************************************** *********

On Wed, Jan 08, 2003 at 11:02:38AM -0800, Dick Beyer wrote: > I installed the affy_1.1.3.zip package and I tried the Laurent expresso patch of Jan 8. I get the following error: > > peter3.eset <- expresso(peter3,normalize.method=FALSE, bgcorrect.method="mas", pmcorrect.method="mas", summary.method="mas") > background correction: mas > normalization: FALSE > PM/MM correction : mas > expression values: mas > background correcting...done. > normalizing...Error in pmatch(x, table, duplicates.ok) : > argument is not of mode character If one does not want normalization, the current way to specify it is to set normalize=FALSE (but the way you tried to do it is kind of intuitive ... will think about it for the next release...) Example data(affybatch.example) ## using that rather than peter3 abatch.n <- expresso(affybatch.example, normalize=FALSE, bgcorrect.method="mas", pmcorrect.method="mas", summary.method="mas") Hopin' it helps, L.