Hi, I have a problem when working with GOSeq. There is support for mm10 genome but not Gene ID geneSymbol I am trying to get length information by following the Goseq manual but I still dont understand. So, could you please show me a little details how to get the length information for mm10 genome and geneID geneSymbol ? >genes = as.integer(all.genes %in% F.genes) > names(genes) = all.genes > head(genes) Cryba1 Cryba4 Cryga Crygb Crygc Crygd 1 1 1 1 1 1 > pwf=nullp(genes,"mm10", "geneSymbol") Can't find mm10/geneSymbol length data in genLenDataBase... Trying to download from UCSC. This might take a couple of minutes. Error in value[[3L]](cond) : Length information for genome mm10 and gene ID geneSymbol is not available. You will have to specify bias.data manually. Thank you so much for your help [[alternative HTML version deleted]]

Hi Thanh, I don't speak for GOSeq specifically. But just very generally if you just want to know the length information for the mm10 genome you could download a transcriptome package and look at the seq lengths for it. Like this: library("Mus.musculus") seqlengths(Mus.musculus) And to get lookup the geneID from the gene symbol you could do it like this symbols <- c('Cryba1','Cryba4','Cryga','Crygb','Crygc','Crygd') select(Mus.musculus, keys=symbols, columns='ENTREZID',keytype='ALIAS') ## OR if you feel more confident that these are official gene symbols then do it like this: select(Mus.musculus, keys=symbols, columns='ENTREZID',keytype='SYMBOL') If you then want gene lengths you can get that too using genes() like this: genes(TxDb.Mmusculus.UCSC.mm10.knownGene) I hope this helps, Marc On 10/24/2013 10:35 AM, Thanh Hoang wrote: > Hi, > I have a problem when working with GOSeq. There is support for mm10 genome but not Gene ID geneSymbol > I am trying to get length information by following the Goseq manual but I still dont understand. So, could you please show me a little details how to get the length information for mm10 genome and geneID geneSymbol ? > >> genes = as.integer(all.genes %in% F.genes) >> names(genes) = all.genes >> head(genes) > Cryba1 Cryba4 Cryga Crygb Crygc Crygd > 1 1 1 1 1 1 >> pwf=nullp(genes,"mm10", "geneSymbol") > Can't find mm10/geneSymbol length data in genLenDataBase... Trying to download from UCSC. This might take a couple of minutes. > Error in value[[3L]](cond) : > Length information for genome mm10 and gene ID geneSymbol is not available. You will have to specify bias.data manually. > Thank you so much for your help > [[alternative HTML version deleted]] > > _______________________________________________ > 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