http://www.bioconductor.org/help/course- materials/2009/SeattleNov09/RNASeq/RNASeqTools.pdf This is the document I found on the web. It is interesting as it has some functions to perform the Bullard et al. UpperQuartile normalisation. I want to see how that transforms transcript counts, hence me carrying out the steps. Typically, just before I get to the interesting bit, it falls down :-). To be honest, it would be really cool if a function was written that take a data frame and upper-quartile normalise the data, using columns as samples and rows as genes. Have I missed that, does that exist? head(yAnno) ensembl_gene_id ensembl_exon_id chr strand start end gene_biotype YHR055C.1 YHR055C YHR055C.1 8 -1 214535 214720 protein_coding YPR161C.1 YPR161C YPR161C.1 16 -1 864445 866418 protein_coding YOL138C.1 YOL138C YOL138C.1 15 -1 61325 65350 protein_coding YDR395W.1 YDR395W YDR395W.1 4 1 1263317 1266151 protein_coding YGR129W.1 YGR129W YGR129W.1 7 1 750405 751052 protein_coding YPR165W.1 YPR165W YPR165W.1 16 1 875364 875993 protein_coding The code I am really interested in seeing how works is: > notZero <- which(rowSums(geneCountsUI) != 0) > upper.quartiles <- apply(geneCountsUI[notZero, + ], 2, function(x) quantile(x, 0.75)) > uq.scaled <- upper.quartiles/sum(upper.quartiles) * + sum(laneCounts) Thanks, John. On Fri, Aug 27, 2010 at 3:21 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > Inside the function, annoData is just the yAnno data.frame. > > The error means that transcript.id - with a default value of > "ensembl_transcript_id" is not part of the names (colnames) of the > yAnno object. > > At this time you should show us > head(yAnno) > and tell us exactly what document you are following. > > Kasper > > On Fri, Aug 27, 2010 at 10:03 AM, Johnny H <ukfriend22@googlemail.com> > wrote: > > Thanks Kasper for that, the command works but... > > > >> yAnnoUI <- makeGeneRepresentation(yAnno, type = "UIgene") > > Error: transcript.id %in% names(annoData) is not TRUE > >> annoData > > Error: object 'annoData' not found > > Where is annoData coming from? > > > > On Fri, Aug 27, 2010 at 2:59 PM, Kasper Daniel Hansen > > <kasperdanielhansen@gmail.com> wrote: > >> > >> This function has been replaced by the more general > >> makeGeneRepresentation. So the call would now be > >> > >> yAnnoUI <- makeGeneRepresentation(yAnno, type = "UIgene") > >> > >> (there are arguments that allow you to set the gene.id and > >> transcript.id but the defaults are set as below). > >> > >> Kasper > >> > >> On Fri, Aug 27, 2010 at 9:48 AM, Johnny H <ukfriend22@googlemail.com> > >> wrote: > >> > Dear Bioconductors, > >> > I am using the Genominator library and work through the > example...until > >> > I > >> > get to here > >> > > >> >> yAnnoUI <- Genominator:::makeUIgenes(yAnno, gene.id = > >> >> "ensembl_gene_id", > >> > transcript.id = "ensembl_transcript_id", verbose = TRUE) > >> > Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : > >> > object 'makeUIgenes' not found > >> > > >> > Please can you advise me how I can use the makeUIgenes method? > >> > Subsequent > >> > steps in the example don't work without this step. > >> > > >> > Thank you. > >> > > >> >> sessionInfo() > >> > R version 2.11.1 (2010-05-31) > >> > i386-pc-mingw32 > >> > locale: > >> > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > >> > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 > >> > LC_NUMERIC=C LC_TIME=English_United > >> > Kingdom.1252 > >> > attached base packages: > >> > [1] grid stats graphics grDevices utils datasets > methods > >> > base > >> > other attached packages: > >> > [1] rtracklayer_1.8.1 RCurl_1.4-3 bitops_1.0-4.1 > >> > Genominator_1.2.0 GenomeGraphs_1.8.0 biomaRt_2.4.0 > >> > RSQLite_0.9-2 DBI_0.2-5 ShortRead_1.6.2 > >> > Rsamtools_1.0.8 lattice_0.18-8 > >> > [12] Biostrings_2.16.9 GenomicRanges_1.0.8 IRanges_1.6.15 > >> > yeastRNASeq_0.0.3 > >> > loaded via a namespace (and not attached): > >> > [1] Biobase_2.8.0 BSgenome_1.16.5 hwriter_1.2 tools_2.11.1 > >> > XML_3.1-1 > >> > > >> > [[alternative HTML version deleted]] > >> > > >> > _______________________________________________ > >> > Bioconductor mailing list > >> > Bioconductor@stat.math.ethz.ch > >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > Search the archives: > >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > [[alternative HTML version deleted]]