Thank you for those other suggestions. I will try some of them out when I get the chance. Incidentally, the problem I ran into with they missing gene IDs was that cummeRbund chokes on cuffdiff results if the GTF file used has some transcripts with no gene ID. On Dec 10, 2012 3:34 PM, "Marc Carlson" <mcarlson@fhcrc.org> wrote: > Unfortunately, if we did that, there could be all sorts of unfortunate > consequences. > > By doing this, you would be introducing an arbitrary number of new strings > as IDs for all of these orphaned transcripts. And unlike NAs (which is the > traditional way of indicating that data is missing in R), you would get no > warnings about any of these when you used them in subsequent analysis. > Others could use your new faux IDs to get into all sorts of trouble. And > would be even worse because they would mixed in with real IDs (entrez gene > IDs) which would lend them a confusing air of authenticity. Downstream > users might even mix the faux IDs from different species etc. > > And even if we accepted the risks, we don't even have a good way of always > grouping the unassigned transcripts, which means that transcripts that are > probably from the same gene will be assigned like this: > > unknown1 = tx1 (overlaps with tx2) > unknown2 = tx2 (overlaps with tx1) > etc. > > Which means that this strategy would also end up implying things that we > know are sometimes not going to be true. Meanwhile these half wrong > unknown transcript assignments will be mixed in with the "real" ones... > > I could go on and on, but I am hoping you can see some of what I am > concerned about? > > > > Anyhow you can already discover about which genes are associated with > transcripts in many other ways. The simplest approach is probably to just > use select() like this: > > library(TxDb.Hsapiens.UCSC.**hg19.knownGene) > txdb = TxDb.Hsapiens.UCSC.hg19.**knownGene > k = keys(txdb, "TXNAME") > res <- select(txdb, cols=c("TXNAME","GENEID"), keys=k, keytype="TXNAME") > head(res) > > > > Alternatively you could ALSO do something like this (if you had previously > already called transcripts like below): > > t <- transcripts(txdb,columns="**gene_id") > as.character(mcols(t)$gene_id) > > > > Marc > > > > > On 12/10/2012 12:25 PM, Ryan C. Thompson wrote: > >> I have also been bitten by the fact that some transcripts are missing >> gene IDs. Is it possible to add placeholder gene IDs to these? For example, >> just assigning them UNKNOWN1, UNKNOWN2, etc.? >> >> On Mon 10 Dec 2012 11:40:35 AM PST, Marc Carlson wrote: >> >>> Hi Matthew, >>> >>> Thanks for your detailed exploration of this. After looking more >>> closely, I think the confusion here is being caused by the fact that you >>> are looking at the kgXref table, and what was actually used to attach >>> gene Ids to the TxDb database is actually the knownToLocusLink >>> <http: genome.ucsc.edu="" cgi-**bin="" hgtables?hgsid="316115443&amp;**">>> hgta_doSchemaDb=hg19&hgta_**doSchemaTable=knownToLocusLink<http: genome.ucsc.edu="" cgi-bin="" hgtables?hgsid="316115443&amp;hgta_doSchemaDb=hg19&amp;" hgta_doschematable="knownToLocusLink"> >>> **> >>> table. Adding to the mayhem, UCSC has apparently decided to allow >>> different values to exist into the latest versions of these two tables. >>> >>> We chose to use the Entrez Gene IDs as gene identifiers because (unlike >>> gene symbols) they represent a real identifier and can thus be relied on >>> to not have multiple different meanings etc. >>> >>> >>> Marc >>> >>> >>> >>> On 12/10/2012 09:06 AM, Matthew D. Wilkerson wrote: >>> >>>> Hello, >>>> >>>> I have a question about the gene_id attribute of >>>> TxDb.Hsapiens.UCSC.hg19.**knownGene, version 2.80 (latest). >>>> >>>> I noticed that some transcripts such as uc021ums.1, do not have an >>>> associated gene_id. >>>> >>>> library(TxDb.Hsapiens.UCSC.**hg19.knownGene) >>>> t=transcripts(txdb,columns=c("**gene_id","tx_id","tx_name","**cds _id","cds_name")) >>>> >>>> >>>> t[ which(elementMetadata(t)[,"tx_**name"]=="uc021ums.1"), ] >>>> >>>> I understand that some ucsc genes might not have an entrez gene id >>>> associated. >>>> I checked this locus and found that currently UCSC db does have this >>>> locus associated with LINGO3. >>>> >>>> #hg19.knownGene.name hg19.knownGene.chrom >>>> hg19.knownGene.strand hg19.knownGene.txStart >>>> hg19.knownGene.txEnd hg19.knownGene.cdsStart >>>> hg19.knownGene.cdsEnd hg19.knownGene.exonCount >>>> hg19.knownGene.exonStarts hg19.knownGene.exonEnds >>>> hg19.knownGene.proteinID hg19.knownGene.alignID >>>> hg19.kgXref.kgID hg19.kgXref.geneSymbol >>>> uc021ums.1 chr19 - 2289996 2291775 2289996 >>>> 2291775 1 2289996, 2291775, P0C6S8 uc021ums.1 >>>> uc021ums.1 LINGO3 >>>> >>>> >>>> The kgXref table was last updated 2/5/12. >>>> >>>> >>>> The bioconductor package was made on: >>>> Creation time: 2012-09-10 12:56:25 -0700 (Mon, 10 Sep 2012) >>>> >>>> If this date also refers to the date of download, then why is this >>>> transcript not affiliated with LINGO3? >>>> If not, then what date does known gene refer to? >>>> >>>> >>>> Thanks, >>>> Matt >>>> >>>> >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >> > [[alternative HTML version deleted]]