>> Error in build.eset(tdPROC, targets, makePLOT = FALSE, >> annotation.package = "hgug4112a.db") : >> rownames in pData(targets) different from colnames RGlist$G >The error message indicates that you don't have the same number of samples data (tdPROC: colnames RGlist$G) as you have information about (targets: pData(targets)). It can also happen when during the analysis you changed the name of the samples (=colnames in RGlist) but did not change the names in your targets file. They should stay be the same. cheers jarek -- Jarek Bryk | www.evolbio.mpg.de/~bryk Max Planck Institute for Evolutionary Biology August Thienemann Str. 2 | 24306 Pl?n, Germany tel. +49 4522 763 287 | bryk at evolbio.mpg.de

Francois, Here is the results... > dim(targets) [1] 3 4 > dim(tdPROC) [1] 41093 3 And here are the filenames and the start of my tdPROC$G for comparison as well. > targets Slide.Number 1 1 2 2 3 3 FileName 1 /Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agilent_ Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_1_006_DS_EP 2 /Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agilent_ Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_2_008_BR_LP 3 /Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agilent_ Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_3_005_EC_NP Treatment GErep 1 EP 1 2 LP 2 3 NP 3 > colnames(tdPROC$G) [1] "/Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agile nt_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_1_006_DS_EP" [2] "/Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agile nt_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_2_008_BR_LP" [3] "/Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agile nt_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_3_005_EC_NP" Thanks for trying to help, Jon Mohl On Fri, Oct 7, 2011 at 10:53 AM, Francois Pepin <francois.pepin at="" sequentainc.com=""> wrote: > Hi Jon, > > You would have to give us some more information about your code. > > The error message indicates that you don't have the same number of samples data (tdPROC: colnames RGlist$G) as you have information about (targets: pData(targets)). > > What sare the result of: > dim(tdPROC) > dim(targets) > > Francois > > On Oct 7, 2011, at 8:03 , Jon Mohl wrote: > >> Hello, >> >> I am currently getting a error when trying to use the build.est >> function of the Agi4x44PreProcess package. ?The error is as follows: >> >> Error in build.eset(tdPROC, targets, makePLOT = FALSE, >> annotation.package = "hgug4112a.db") : >> ?rownames in pData(targets) different from colnames RGlist$G >> >> Here is the command I have given: >> >> esetPROC = build.eset(tdPROC, targets, makePLOT = FALSE, >> annotation.package="hgug4112a.db") >> >> >> I have followed the example within the Agi4x44PreProcess.pdf manual, >> and thus far this is the only problem I have run into. ?For reference, >> I am running R 2.10.1. >> >> Thanks for your help, >> >> Jon Mohl >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >