I am using R.1.9.0 upgraded to affy 1.4.29, Biobase 1.4.14. I get the following error below with rma() and mas5() functions and tried to figure out what is happening all afternoon. I tried it with a couple of datasets with the same results. Can anyone help ? Thank you, Adai. > library(affy) Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. > library(gcrma) > data <- ReadAffy() > data AffyBatch object size of arrays=536x536 features (134681 kb) cdf=Hu6800 (7129 affyids) number of samples=60 number of genes=7129 annotation=hu6800 > print(date()) [1] "Tue May 18 18:16:42 2004" > > data.rma <- rma( data ) Error in mget(genenames, pos, envir, iffail = NA) : unused argument(s) (iffail ...) > data1.mas5 <- mas5(data1) background correction: mas PM/MM correction : mas expression values: mas background correcting...Error in mget(genenames, pos, envir, iffail = NA) : unused argument(s) (iffail ...) Execution halted

You should upgrade to affy 1.4.30, which doesn't have this bug. Best, 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 >>> Adaikalavan Ramasamy <ramasamy@cancer.org.uk> 05/18/04 01:29PM >>> I am using R.1.9.0 upgraded to affy 1.4.29, Biobase 1.4.14. I get the following error below with rma() and mas5() functions and tried to figure out what is happening all afternoon. I tried it with a couple of datasets with the same results. Can anyone help ? Thank you, Adai. > library(affy) Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. > library(gcrma) > data <- ReadAffy() > data AffyBatch object size of arrays=536x536 features (134681 kb) cdf=Hu6800 (7129 affyids) number of samples=60 number of genes=7129 annotation=hu6800 > print(date()) [1] "Tue May 18 18:16:42 2004" > > data.rma <- rma( data ) Error in mget(genenames, pos, envir, iffail = NA) : unused argument(s) (iffail ...) > data1.mas5 <- mas5(data1) background correction: mas PM/MM correction : mas expression values: mas background correcting...Error in mget(genenames, pos, envir, iffail = NA) : unused argument(s) (iffail ...) Execution halted _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor