Dear all, I want to analyse my affy data with limma. I have 3 genotypes A, B, C I want to compare to the reference ref, and 3 replicates for each genotype and ref, so 12 arrays. I have this error message I don t understand: > data<-ReadAffy() > eset<-rma(data) > design ref A B C Exp143hyb246 1 0 0 0 Exp143hyb247 1 1 0 0 Exp143hyb248 1 0 1 0 Exp143hyb249 1 0 0 1 Exp143hyb410 1 0 0 0 Exp143hyb411 1 0 0 0 Exp143hyb412 1 1 0 0 Exp143hyb413 1 1 0 0 Exp143hyb414 1 0 1 0 Exp143hyb415 1 0 1 0 Exp143hyb416 1 0 0 1 Exp143hyb417 1 0 0 1 > fit<-lm.series(exprs(eset), design) Error in as.double.default(structure(list(ler = c(1, 1, 1, 1, 1, 1, 1, : (list) object cannot be coerced to vector type 14 What's wrong with my design ? Thanks Delphine -- ================================================================== Delphine Fleury DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium Vlaams Interuniversitair Instituut voor Biotechnologie VIB mailto:defle@psb.ugent.be http://www.psb.ugent.be

Dear Delphine, How exactly did you create "design"? Try d1 <- as.matrix(design) and then using d1 in lm.series. Ram?n On Thursday 21 August 2003 14:51, Delphine Fleury wrote: > Dear all, > I want to analyse my affy data with limma. I have 3 genotypes A, B, C I > want to compare to the reference ref, and 3 replicates for each genotype > > and ref, so 12 arrays. I have this error message I don t understand: > > data<-ReadAffy() > > eset<-rma(data) > > > > design > > ref A B C > Exp143hyb246 1 0 0 0 > Exp143hyb247 1 1 0 0 > Exp143hyb248 1 0 1 0 > Exp143hyb249 1 0 0 1 > Exp143hyb410 1 0 0 0 > Exp143hyb411 1 0 0 0 > Exp143hyb412 1 1 0 0 > Exp143hyb413 1 1 0 0 > Exp143hyb414 1 0 1 0 > Exp143hyb415 1 0 1 0 > Exp143hyb416 1 0 0 1 > Exp143hyb417 1 0 0 1 > > > fit<-lm.series(exprs(eset), design) > > Error in as.double.default(structure(list(ler = c(1, 1, 1, 1, 1, 1, 1, > > (list) object cannot be coerced to vector type 14 > > What's wrong with my design ? > Thanks > > Delphine > > > > > -- > ================================================================== > Delphine Fleury > DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 > GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium > Vlaams Interuniversitair Instituut voor Biotechnologie VIB > mailto:defle@psb.ugent.be http://www.psb.ugent.be > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz

Dear Delphine, At 10:51 PM 21/08/2003, Delphine Fleury wrote: >Dear all, >I want to analyse my affy data with limma. I have 3 genotypes A, B, C I >want to compare to the reference ref, and 3 replicates for each genotype >and ref, so 12 arrays. I have this error message I don t understand: > > > data<-ReadAffy() > > eset<-rma(data) > > > design > ref A B C >Exp143hyb246 1 0 0 0 >Exp143hyb247 1 1 0 0 >Exp143hyb248 1 0 1 0 >Exp143hyb249 1 0 0 1 >Exp143hyb410 1 0 0 0 >Exp143hyb411 1 0 0 0 >Exp143hyb412 1 1 0 0 >Exp143hyb413 1 1 0 0 >Exp143hyb414 1 0 1 0 >Exp143hyb415 1 0 1 0 >Exp143hyb416 1 0 0 1 >Exp143hyb417 1 0 0 1 > > > fit<-lm.series(exprs(eset), design) The 'design' argument to lm.series needs to be a numeric matrix. Your 'design' is a data.frame, as can be seen by the fact that it contains both character and numeric elements. You need design <- as.matrix(design[,-1]) and then proceed to 'lm.series'. (Note that as.matrix(design) will not work as it will give you a character matrix!) If you install the development version of limma, then you could use fit <- lmFit(eset, design) i.e., lmFit will work directly on exprSet objects. Regards Gordon >Error in as.double.default(structure(list(ler = c(1, 1, 1, 1, 1, 1, 1, >: > (list) object cannot be coerced to vector type 14 > >What's wrong with my design ? >Thanks > >Delphine > > > > >-- >================================================================== >Delphine Fleury >DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 >GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium >Vlaams Interuniversitair Instituut voor Biotechnologie VIB >mailto:defle@psb.ugent.be http://www.psb.ugent.be