hi all, i'm debating on whether to download GO annotations through biomart or just get them from GO directly. The advantage to me of getting it through biomart is that i can get the ID format i need right away. However, when i compare the annotations from Biomart, versus GO directly, there seems to be a huge discrepancy, mainly in two areas: 1) # of annotations - direct download from GO seems to obtain hundreds of thousands more annotations. 2) evidence types - biomart seems to not use a lot of the evidence codes that i find from the direct-GO approach, mostly from the 'computational analysis' evidence codes. both #1 and #2 leads me to think Biomart doesn't update its annotations often, but i'm not sure if i'm just not grabbing it correctly -- does anyone know how often they update? [[alternative HTML version deleted]]

Hi Brian, There is also the GO.db package. As for which resource will work best for you, that will really depend on what you need more: very current annotations or the stability of a version-ed release? You have a whole range of options here. GO will always be the most current, but really, biomaRt is usually very current as well. If you have found discrepancies please provide a reproducible example that people can test. Marc On 11/02/2011 03:53 PM, Brian Tsai wrote: > hi all, > > i'm debating on whether to download GO annotations through biomart or just > get them from GO directly. The advantage to me of getting it through > biomart is that i can get the ID format i need right away. However, when i > compare the annotations from Biomart, versus GO directly, there seems to be > a huge discrepancy, mainly in two areas: > > 1) # of annotations - direct download from GO seems to obtain hundreds of > thousands more annotations. > 2) evidence types - biomart seems to not use a lot of the evidence codes > that i find from the direct-GO approach, mostly from the 'computational > analysis' evidence codes. > > > both #1 and #2 leads me to think Biomart doesn't update its annotations > often, but i'm not sure if i'm just not grabbing it correctly -- does > anyone know how often they update? > > [[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