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Hi Jason, Not sure if this is the problem, but your affy and affyio packages are slightly out of date. Try library(Biobase) repos <- biocReposList() update.packages(repos=repos, ask=FALSE) and see if that fixes things. Best, Jim Jason Pear wrote: > Dear List, > > I am new in this field, and I currently faced this error when I tried the > mas5 and gcrma functions. I really appreciate your helps. > > Here are the partial R codes and error messages: > > > # --------------------------------------- > >> mas5.expSet <- mas5(celData); > > background correction: mas > > PM/MM correction : mas > > expression values: mas > > background correcting...Error in as.vector(data) : NA/NaN/Inf in foreign > function call (arg 1) > > > >> gcrma.expSet <- gcrma(celData); > > Adjusting for optical effect.....Done. > > Computing affinities.Error in matrix(NA, nrow = max(cbind(pmIndex, > mmIndex)), ncol = 1) : > > matrix: invalid 'nrow' value (too large or NA) > > > >> sessionInfo() > > R version 2.5.0 (2007-04-23) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > "datasets" "methods" "base" > > > > other attached packages: > > citrusprobe citruscdf LPE affycoretools annaffy > xtable biomaRt RCurl XML GOstats Category > > > "1.16.0" "1.16.0" "1.10.0" "1.8.0" "1.8.1" > "1.4-6" "1.10.0" "0.8-0" "1.7-1" "2.2.5" "2.2.3" > > > Matrix lattice genefilter survival KEGG > RBGL annotate GO graph limma gcrma > > "0.99875-1" "0.15-4" "1.14.1" "2.31" "1.16.0" " > 1.12.0" "1.14.1" "1.16.0" "1.14.2" "2.10.5" "2.8.1" > > > matchprobes affydata affy affyio Biobase > "1.8.1" "1.11.2" "1.14.1" "1.4.0" "1.14.0" > > Many thanks, > > Jason > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623