If I ask for the chromosome location of the start of geneID 5004, I get: > get ('5004', org.Hs.egCHRLOC) 9 116125123 But geneID 20 gets me two identical values: > get ('20', org.Hs.egCHRLOC) 9 9 -139021506 -139021506 I noticed this after using toTable to create a data.frame from this environment: I get two identical rows for geneID 20: > subset (toTable (org.Hs.egCHRLOC), gene_id=='20') gene_id start_location Chromosome 14 20 -139021506 9 15 20 -139021506 9 Is this the expected behavior? Thanks! - Paul

On Mon, Mar 9, 2009 at 8:26 AM, Paul Shannon <pshannon@systemsbiology.org>wrote: > If I ask for the chromosome location of the start of geneID 5004, I get: > > > get ('5004', org.Hs.egCHRLOC) > 9 > 116125123 > > But geneID 20 gets me two identical values: > > > get ('20', org.Hs.egCHRLOC) > 9 9 > -139021506 -139021506 > > I noticed this after using toTable to create a data.frame from this > environment: I get two identical rows for geneID 20: > > > subset (toTable (org.Hs.egCHRLOC), gene_id=='20') > gene_id start_location Chromosome > 14 20 -139021506 9 > 15 20 -139021506 9 > > Is this the expected behavior? > Yep. Gene ID "20" has two transcripts and both start at the same location. Gene ID "5004" has only one transcript. So, the CHRLOCs are really the transcript starts associated with the gene. Sean [[alternative HTML version deleted]]