Question: Agi4x44PreProcess package: Error in build.est
0
8.0 years ago by
Jon Mohl20
Jon Mohl20 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$G Here is the command I have given: esetPROC = build.eset(tdPROC, targets, makePLOT = FALSE, annotation.package="hgug4112a.db") I have followed the example within the Agi4x44PreProcess.pdf manual, and thus far this is the only problem I have run into. For reference, I am running R 2.10.1. Thanks for your help, Jon Mohl agi4x44preprocess • 496 views ADD COMMENTlink modified 8.0 years ago by Francois Pepin80 • written 8.0 years ago by Jon Mohl20 Answer: Agi4x44PreProcess package: Error in build.est 0 8.0 years ago by Francois Pepin80 wrote: Hi Jon, You would have to give us some more information about your code. The error message indicates that you don't have the same number of samples data (tdPROC: colnames RGlist$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$G > > Here is the command I have given: > > esetPROC = build.eset(tdPROC, targets, makePLOT = FALSE, > annotation.package="hgug4112a.db") > > > I have followed the example within the Agi4x44PreProcess.pdf manual, > and thus far this is the only problem I have run into. For reference, > I am running R 2.10.1. > > Thanks for your help, > > Jon Mohl > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ADD COMMENTlink written 8.0 years ago by Francois Pepin80 >> Error in build.eset(tdPROC, targets, makePLOT = FALSE, >> annotation.package = "hgug4112a.db") : >> rownames in pData(targets) different from colnames RGlist$G >The error message indicates that you don't have the same number of samples data (tdPROC: colnames RGlist$G) as you have information about (targets: pData(targets)). It can also happen when during the analysis you changed the name of the samples (=colnames in RGlist) but did not change the names in your targets file. They should stay be the same. cheers jarek -- Jarek Bryk | www.evolbio.mpg.de/~bryk Max Planck Institute for Evolutionary Biology August Thienemann Str. 2 | 24306 Pl?n, Germany tel. +49 4522 763 287 | bryk at evolbio.mpg.de ADD REPLYlink written 8.0 years ago by Jarek Bryk110 Francois, Here is the results... > dim(targets) [1] 3 4 > dim(tdPROC) [1] 41093 3 And here are the filenames and the start of my tdPROC$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$G >> >> Here is the command I have given: >> >> esetPROC = build.eset(tdPROC, targets, makePLOT = FALSE, >> annotation.package="hgug4112a.db") >> >> >> I have followed the example within the Agi4x44PreProcess.pdf manual, >> and thus far this is the only problem I have run into. ?For reference, >> I am running R 2.10.1. >> >> Thanks for your help, >> >> Jon Mohl >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > ADD REPLYlink written 8.0 years ago by Jon Mohl20 Hi Jon, Have you tried Jeryk's suggestion in making sure that the name match? Right now they're not matching properly. Francois On Oct 9, 2011, at 7:13 , Jon Mohl wrote: > Francois, > > Here is the results... > >> dim(targets) > [1] 3 4 >> dim(tdPROC) > [1] 41093 3 > > And here are the filenames and the start of my tdPROC$G for comparison as well. > >> targets > Slide.Number > 1 1 > 2 2 > 3 3 > > > FileName > 1 /Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agilen t_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_1_006_DS_EP > 2 /Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agilen t_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_2_008_BR_LP > 3 /Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agilen t_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_Agi lent_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_1_006_DS_EP" > [2] "/Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agi lent_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_2_008_BR_LP" > [3] "/Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agi lent_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_3_005_EC_NP" > > Thanks for trying to help, > > Jon Mohl >