Dear list I'm trying to do a rank porducts analysis on an expression set and I cannot get the gene names onto the results table. The error is 'gene.names should have the same length as the gene vector' but I'm giving topGene column 0 of the data matrix I gave RP so how can they have different lengths? What exactly is the 'gene vector' mentioned in the error? My working below. Many thanks for you time. John > class(lumidataB.bgt) [1] "LumiBatch" attr(,"package") [1] "lumi" > e <- exprs(lumidataB.bgt) > head(e) 17 18 19 20 21 22 23 24 Ku8QhfS0n_hIOABXuE 7.2 7.2 7.1 7.2 7.2 7.3 7.1 7.2 fqPEquJRRlSVSfL.8A 7.3 7.3 7.3 7.5 7.3 7.4 7.4 7.4 ckiehnugOno9d7vf1Q 7.3 7.2 7.2 7.3 7.3 7.2 7.3 7.3 x57Vw5B5Fbt5JUnQkI 7.2 7.4 7.2 7.3 7.3 7.3 7.1 7.3 ritxUH.kuHlYqjozpE 7.3 7.3 7.3 7.1 7.1 7.4 7.3 7.3 QpE5UiUgmJOJEkPXpc 7.2 7.2 7.2 7.2 7.4 7.2 7.2 7.2 > design <- c(0,0,0,0,1,1,1,1) > rp.out<-RP(e,design,logged=TRUE,plot=TRUE, num.perm = 100) Rank Product analysis for two-class case Starting 100 permutations... Computing pfp .. Outputing the results .. > topGene(rp.out, cutoff=0.005, method="pfp",gene.names=e[,0]) Warning: gene.names should have the same length as the gene vector. No gene.names are assigned > sessionInfo() R version 2.10.1 (2009-12-14) i386-redhat-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets [6] methods base other attached packages: [1] RankProd_2.18.0 lumiHumanAll.db_1.8.1 [3] org.Hs.eg.db_2.3.6 beadarray_1.14.0 [5] lumiHumanIDMapping_1.4.0 lumi_1.12.4 [7] MASS_7.3-4 RSQLite_0.8-4 [9] DBI_0.2-5 preprocessCore_1.8.0 [11] mgcv_1.6-1 annotate_1.24.1 [13] AnnotationDbi_1.8.2 affy_1.24.2 [15] Biobase_2.6.1 limma_3.2.3 loaded via a namespace (and not attached): [1] affyio_1.14.0 grid_2.10.1 hwriter_1.2 [4] KernSmooth_2.23-3 lattice_0.17-26 Matrix_0.999375-33 [7] nlme_3.1-96 tools_2.10.1 xtable_1.5-6 _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. [[alternative HTML version deleted]]

Hi John -- On 05/13/2010 02:09 AM, John Coulthard wrote: > > Dear list > > I'm trying to do a rank porducts analysis on an expression set and I cannot get the gene names onto the results table. The error is 'gene.names should have the same length as the gene vector' but I'm giving topGene column 0 of the data matrix I gave RP so how can they have different lengths? What exactly is the 'gene vector' mentioned in the error? > > My working below. > Many thanks for you time. > > John > >> class(lumidataB.bgt) > [1] "LumiBatch" > attr(,"package") > [1] "lumi" >> e <- exprs(lumidataB.bgt) >> head(e) > 17 18 19 20 21 22 23 24 > Ku8QhfS0n_hIOABXuE 7.2 7.2 7.1 7.2 7.2 7.3 7.1 7.2 > fqPEquJRRlSVSfL.8A 7.3 7.3 7.3 7.5 7.3 7.4 7.4 7.4 > ckiehnugOno9d7vf1Q 7.3 7.2 7.2 7.3 7.3 7.2 7.3 7.3 > x57Vw5B5Fbt5JUnQkI 7.2 7.4 7.2 7.3 7.3 7.3 7.1 7.3 > ritxUH.kuHlYqjozpE 7.3 7.3 7.3 7.1 7.1 7.4 7.3 7.3 > QpE5UiUgmJOJEkPXpc 7.2 7.2 7.2 7.2 7.4 7.2 7.2 7.2 > >> design <- c(0,0,0,0,1,1,1,1) >> rp.out<-RP(e,design,logged=TRUE,plot=TRUE, num.perm = 100) > Rank Product analysis for two-class case > > Starting 100 permutations... > Computing pfp .. > Outputing the results .. >> topGene(rp.out, cutoff=0.005, method="pfp",gene.names=e[,0]) e[,0] returns a matrix of length 0 > library(Biobase) > data(sample.ExpressionSet) > length(exprs(sample.ExpressionSet)[,0]) [1] 0 whereas I think what you want is a character vector of length nrow(e) > length(rownames(exprs(sample.ExpressionSet))) [1] 500 > length(featureNames(sample.ExpressionSet)) [1] 500 Martin > Warning: gene.names should have the same length as the gene vector. > No gene.names are assigned > > > > >> sessionInfo() > R version 2.10.1 (2009-12-14) > i386-redhat-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets > [6] methods base > > other attached packages: > [1] RankProd_2.18.0 lumiHumanAll.db_1.8.1 > [3] org.Hs.eg.db_2.3.6 beadarray_1.14.0 > [5] lumiHumanIDMapping_1.4.0 lumi_1.12.4 > [7] MASS_7.3-4 RSQLite_0.8-4 > [9] DBI_0.2-5 preprocessCore_1.8.0 > [11] mgcv_1.6-1 annotate_1.24.1 > [13] AnnotationDbi_1.8.2 affy_1.24.2 > [15] Biobase_2.6.1 limma_3.2.3 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 grid_2.10.1 hwriter_1.2 > [4] KernSmooth_2.23-3 lattice_0.17-26 Matrix_0.999375-33 > [7] nlme_3.1-96 tools_2.10.1 xtable_1.5-6 > > > > > _________________________________________________________________ > Hotmail: Trusted email with Microsoft?s powerful SPAM protection. > > [[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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793