Hi Dick, I believe the problem is fixed in the version of simpleaffy in the Devl branch (2.07). I'll also update the release version - in the meantime try the version from the devl release. Cheers, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Dick Beyer Sent: 19 January 2005 00:03 To: Bioconductor Subject: [BioC] Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: moe430acdf I am getting an error when I try the simpleaffy routine qc() on a set of moe430a chips. exp1.all.raw <- ReadAffy(widget=T) exp1.all.raw AffyBatch object size of arrays=712x712 features (51493 kb) cdf=MOE430A (22690 affyids) number of samples=13 number of genes=22690 annotation=moe430a exp1.mas5 <- call.exprs(exp1.all.raw,"mas5") qc <- qc(exp1.all.raw,exp1.mas5) Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: moe430acdf qc.affy calls haveQCParams, but haveQCParams shows: > rownames(get("alpha", envir = .qcEnv)) [1] "atgenomecdf" "ath1121501cdf" "drosgenome1cdf" "hcg110cdf" "hgfocuscdf" [6] "hgu133acdf" "hgu133a2cdf" "hgu133atagcdf" "hgu133bcdf" "hgu133plus2cdf" [11] "hgu95acdf" "hgu95av2cdf" "hgu95bcdf" "hgu95ccdf" "hgu95dcdf" [16] "hgu95ecdf" "mgu74acdf" "mgu74av2cdf" "mgu74bcdf" "mgu74bv2cdf" [21] "mgu74ccdf" "mgu74cv2cdf" "mouse4302cdf" "mouse430acdf" "mouse430a2cdf" [26] "mouse430b2cdf" "mu11ksubacdf" "mu11ksubbcdf" "rae230acdf" "rae230bcdf" [31] "rgu34acdf" "rgu34bcdf" "rgu34ccdf" "ygs98cdf" "zebrafishcdf" [36] "rat2302cdf" so qc() is expecting mouse430a, instead, it gets moe430a. I remember some discussion of this issue some time ago, but was unable to find it in the mail archives. My windows packages are: base 2.0.1 datasets 2.0.1 utils 2.0.1 grDevices 2.0.1 graphics 2.0.1 stats 2.0.1 methods 2.0.1 tools 2.0.1 Biobase 1.5.0 reposTools 1.5.1 affy 1.5.8 matchprobes 1.0.12 gcrma 1.1.1 qvalue 1.1 siggenes 1.2.11 limma 1.8.6 GO 1.6.4 KEGG 1.6.2 annotate 1.5.1 annaffy 1.0.11 moe430a 1.6.8 moe430acdf 1.4.3 moe430aprobe 1.0 simpleaffy 2.01 tcltk 2.0.1 widgetTools 1.4.7 DynDoc 1.5.0 tkWidgets 1.5.20 xtable 1.2-4 Thanks very much for any help or suggestions. Thanks, Dick ********************************************************************** ** ******* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}