Hi again, I'm analyzing an experiment that uses MOE430A chips on R1.9.1 and GCRMA 1.1.0 on a windows machine. I get an error message from GCRMA of: > eset <- gcrma(eset); Computing affinitiesError in get(x, envir, mode, inherits) : variable "moe430aprobe" was not found > traceback(); 3: get(probepackagename) 2: compute.affinities(cdfName(object), verbose = verbose) 1: gcrma(eset) This issue does *not* occur with other chip-types (see below) and doesn't go away if I load the probe-library with library() (also see below). The problem does not seem to depend on the specific CEL-files, as I have used over 40 different files and they all seem to exhibit this problem. Any suggestions on what might be going wrong here? Any additional data I can/ should provide? Paul # Try to process MOE430A files > cel.files <- c( + '2(1b)MOE430A_081904_MS01T_LH.CEL', + '2(2b)MOE430A_081904_MS02T_LH.CEL', + '2(3)MOE430A_012904_MS01T_LH.CEL', + '2(4)MOE430A_012904_MS02T_LH.CEL', + '2(5)MOE430A_012904_MS03T_LH.CEL', + ); > eset <- ReadAffy(filenames=cel.files); > eset; AffyBatch object size of arrays=712x712 features (19806 kb) cdf=MOE430A (22690 affyids) number of samples=5 number of genes=22690 annotation=moe430a > eset <- gcrma(eset); Computing affinitiesError in get(x, envir, mode, inherits) : variable "moe430aprobe" was not found > traceback(); 3: get(probepackagename) 2: compute.affinities(cdfName(object), verbose = verbose) 1: gcrma(eset) # Try to manually load probe library > library(moe430aprobe); > eset <- gcrma(eset); Computing affinitiesError in get(x, envir, mode, inherits) : variable "moe430aprobe" was not found # Try this on RAE230-2 arrays > setwd("../test"); > eset <- ReadAffy(); > eset Attaching package 'rat2302cdf': The following object(s) are masked from package:moe430acdf : i2xy xy2i AffyBatch object size of arrays=834x834 features (16306 kb) cdf=Rat230_2 (31099 affyids) number of samples=3 number of genes=31099 annotation=rat2302 # and it succeeds! > eset <- gcrma(eset); Computing affinities.Done. Adjusting for optical effect...Done. Adjusting for non-specific binding...Done. Normalizing Calculating Expression

paul.boutros@utoronto.ca wrote: > Hi again, > > I'm analyzing an experiment that uses MOE430A chips on R1.9.1 and GCRMA 1.1.0 on > a windows machine. I get an error message from GCRMA of: > > >>eset <- gcrma(eset); > > Computing affinitiesError in get(x, envir, mode, inherits) : variable > "moe430aprobe" was not found > This is due to the fact that there is a zipped file that is being choked on. You can get things to work if you simply go to C:\path_to_R\library\moe430aprobe\data and unzip the Rdata.zip file you will find there. In the meantime I will make another moe430aprobe file that doesn't have the zipped data file. This should be on the BioC website in the next day or so. 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