Dear colleagues, I would like to check if my understanding onone aspect of GOstats is correct. The probeset 1370428_x_at is linked to the GO term GO:0002474 When I use hyperGTest (with conditional=F), if this probeset is DE, enrichment of GO:0002474 will be tested. And so will its parent GO term GO:0048002, even this GO term is not explicitly linked to the affy id in the annotation. Is that correct? GOstats will follow the GO tree from bottom-up to conduct tests? On a slightly different matter, the grandparent node of GO:0002474, GO:0019882, is explicitly linked to this affy id in the annotation. Why is this so, but not the parent node GO:0048002? Many thanks, Alex -------------------------------------------- Alex C. Lam Roslin Institute (Edinburgh) Midlothian EH25 9PS United Kingdom Tel: +44 131 5274471 Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT registration number 847380013. The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute

Hi Alex, alex lam (RI) wrote: > Dear colleagues, > > I would like to check if my understanding onone aspect of GOstats is > correct. > > The probeset 1370428_x_at is linked to the GO term GO:0002474 > > When I use hyperGTest (with conditional=F), if this probeset is DE, > enrichment of GO:0002474 will be tested. And so will its parent GO term > GO:0048002, even this GO term is not explicitly linked to the affy id in > the annotation. Is that correct? GOstats will follow the GO tree from > bottom-up to conduct tests? Yes. Although this particular probeset isn't mapped directly to the parent GO term, it _is_ by definition mapped to that term since the child term is a subset of the parent (here subset being defined by either an is_a or a part_of relationship to the parent). Note that this will be true even if conditional = TRUE, unless GO:0002474 is significant _and_ that particular probeset contributed to that significance. Although we shouldn't be talking about probesets here because the GO analysis is done on the gene level. > > On a slightly different matter, the grandparent node of GO:0002474, > GO:0019882, is explicitly linked to this affy id in the annotation. Why > is this so, but not the parent node GO:0048002? Good question, but wrong forum. We just repackage existing annotations, and as far as I can tell everybody says the same thing about this gene. For instance, NCBI: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=24737 The same thing is true of Affy and Ensembl. Best, Jim > > Many thanks, > Alex > > -------------------------------------------- > Alex C. Lam > Roslin Institute (Edinburgh) > Midlothian > EH25 9PS > United Kingdom > Tel: +44 131 5274471 > > Roslin Institute is a company limited by guarantee, registered in > Scotland (registered number SC157100) and a Scottish Charity (registered > number SC023592). Our registered office is at Roslin, Midlothian, EH25 > 9PS. VAT registration number 847380013. > > The information contained in this e-mail (including any attachments) is > confidential and is intended for the use of the addressee only. The > opinions expressed within this e-mail (including any attachments) are > the opinions of the sender and do not necessarily constitute those of > Roslin Institute (Edinburgh) ("the Institute") unless specifically > stated by a sender who is duly authorised to do so on behalf of the > Institute > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623