Dear expert, I am using Deseq2 and Dexseq to analysis my RNA-seq data. I totally follow the vignette in these packages. In the last output, for the function DEXSeqHTML or HTMLReport, I prefer to use gene symbol, not ensembl ID. For example, I prefer Muc2 to ENSMUSG00000095400. It is more human readable. How can I output gene symbol than Ensembl ID? But it seems that I cannot directly change the gtf file. Because several Ensembl ID match on gene symbol as follow: ENSMUSG00000095400 Muc2 ENSMUSG00000094393 Muc2 ENSMUSG00000025515 Muc2 Thank you very much in advance.

Hello Fabrice Tourre, You can try this. Regards Vang ####R code for fetching gene names with biomaRt ##### require(biomaRt) annot.table <- data.frame() # This is your annotation table, it can't be NULL # Collect ensembl IDs from annot.table before converting to normal gene names. ensembl_ids <- character() # Get this from may be from annot.table # Prepare gene table with some simple caching to avoid stressing the Ensembl server by many repeated runs genes.table = NULL if (!file.exists("cache.genes.table")) { message("Retrieving genes table from Ensembl...") mart <- useMart("ensembl") #listDatasets(mart=mart) mart <- useDataset("hsapiens_gene_ensembl", mart = mart) genes.table <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id", "external_gene_id", "description"), values= ensembl_ids, mart= mart) save(genes.table, file= "cache.genes.table") } else { load("cache.genes.table") message("Reading gene annotation information from cache file: cache/cache.genes.table Remove the file if you want to force retrieving data from Ensembl") } # Merging two tables, syntax showed here are in full forms, by.x and by.y can be simplified annot.table <- merge(x = annot.table, y = genes.table, by.x = "ensembl_id", by.y = "ensembl_gene_id", all.x = T, all.y = F ) # Do something with the table, i.e export to TSV -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Fabrice Tourre Sent: Friday, August 08, 2014 9:18 AM To: Bioconductor mailing list Subject: [BioC] deseq2: convert ensembl ID to gene symbol. Dear expert, I am using Deseq2 and Dexseq to analysis my RNA-seq data. I totally follow the vignette in these packages. In the last output, for the function DEXSeqHTML or HTMLReport, I prefer to use gene symbol, not ensembl ID. For example, I prefer Muc2 to ENSMUSG00000095400. It is more human readable. How can I output gene symbol than Ensembl ID? But it seems that I cannot directly change the gtf file. Because several Ensembl ID match on gene symbol as follow: ENSMUSG00000095400 Muc2 ENSMUSG00000094393 Muc2 ENSMUSG00000025515 Muc2 Thank you very much in advance. _______________________________________________ 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