Hi! I am trying to analyze two-colour cDNA arrays, with the simplest possible design, four replicates, no dye-swaps, treatment =Cy5, ctrl=Cy3. I used printtipWeights function on my normalized data >printtipw=printtipWeights(MAmu3A) Then I used asMatrixWeights function and multiplied printTipWeights and printtipweights >2mu3<-asMatrixWeights(printtipw,c(31200,4)) >combwmu3<-w2mu3*MAmu3A$weights At least that's what I wanted to... Then, according to limma guide examples, I wanted to exclude control and empty spots from my analysis, so I used spottype Status, previously assigned >isGene<-MAmu3A$genes$Status == "cDNA" But I can not put it in one lmFit command with the combined weights: > fitmu3<-lmFit(MAmu3A[isGene, ], weights=combwmu3) Error in asMatrixWeights(weights, dim(M)) : weights is of unexpected shape However, I can use lmFit function without combwmu3, or with combwmu3, but not excluding control and empty spots: > fitmu3<-lmFit(MAmu3A[isGene, ]) or > fitmu3comb<-lmFit(MAmu3A, weights=combwmu3) please help me deal with it, cause I am not creative when considering R enviroment.... Many thanks Agnieszka Dr Agnieszka ¯mieñko Centrum Doskonalosci CENAT Instytut Chemii Bioorganicznej Polskiej Akademii Nauk Noskowskiego 12/14 61-704 Poznañ tel. (61) 8528503 wew. 249 fax: (61) 8520532 Agnieszka Zmienko, Ph.D. CENAT Institute of Bioorganic Chemistry Polish Academy of Sciences Noskowskiego 12/14 61-704 Poznan, Poland phone (0048) 61-8528503 ext. 249 fax: (0048) 61-8520532 [[alternative HTML version deleted]]

Dear Agnieszka I have not tried this, but I think you want to do the 'isGene' subsetting synchronously with 'MAmu3A' and 'combwmu3', i.e. fitmu3 <- lmFit(object = MAmu3A[isGene, ], weights = combwmu3[isGene, ]) Btw, next time please provide a reproducible example, and the output of sessionInfo(). Best wishes Wolfgang Zmienko wrote: > Hi! > I am trying to analyze two-colour cDNA arrays, > with the simplest possible design, four > replicates, no dye-swaps, treatment =Cy5, ctrl=Cy3. > > I used printtipWeights function on my normalized data > > >printtipw=printtipWeights(MAmu3A) > > Then I used asMatrixWeights function and > multiplied printTipWeights and printtipweights > > >2mu3<-asMatrixWeights(printtipw,c(31200,4)) > >combwmu3<-w2mu3*MAmu3A$weights > > At least that's what I wanted to... > > Then, according to limma guide examples, I wanted > to exclude control and empty spots from my > analysis, so I used spottype Status, previously assigned > > >isGene<-MAmu3A$genes$Status == "cDNA" > > > But I can not put it in one lmFit command with the combined weights: > > > fitmu3<-lmFit(MAmu3A[isGene, ], weights=combwmu3) > Error in asMatrixWeights(weights, dim(M)) : > weights is of unexpected shape > > However, I can use lmFit function without > combwmu3, or with combwmu3, but not excluding control and empty spots: > > > fitmu3<-lmFit(MAmu3A[isGene, ]) > or > > fitmu3comb<-lmFit(MAmu3A, weights=combwmu3) > > please help me deal with it, cause I am not > creative when considering R enviroment.... > > Many thanks > > Agnieszka > > > > Dr Agnieszka ?mie?ko > > Centrum Doskonalosci CENAT > Instytut Chemii Bioorganicznej Polskiej Akademii Nauk > Noskowskiego 12/14 > 61-704 Pozna? > tel. (61) 8528503 wew. 249 > fax: (61) 8520532 > > Agnieszka Zmienko, Ph.D. > > CENAT > Institute of Bioorganic Chemistry > Polish Academy of Sciences > Noskowskiego 12/14 > 61-704 Poznan, Poland > phone (0048) 61-8528503 ext. 249 > fax: (0048) 61-8520532 > [[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 -- Best wishes Wolfgang ------------------------------------------------------- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber