I found no of homology pairs in R homology package is different from http://inparanoid.sbc.su.se/download/current/table_stats/ For example, there are 1804 homo-sapien-Spombe pairs in Hom.Hs.inp.db, inparanoid website claims, 5615 sequences H.sapiens.fa have homologs in dataset S.pombe.fa 2986 sequences S.pombe.fa have homologs in dataset H.sapiens.fa May I know did you apply any cutoff for the homology pairs in R package? -- output of sessionInfo(): .. -- Sent via the guest posting facility at bioconductor.org.

Hi Rachel, That's a good question to be asking if you want to make use of these packages. If you are looking at the inpararanoid packages, the bimap objects will only expose the mappings that inparanoid indicates are perfectly matched. If that is too conservative for you, the database inside has all of the available data for mappings. I am not really sure where you are getting 1804 from, but if you use the bimap you will only get the most conservative mappging. So for example: dim(toTable(hom.Hs.inpSCHPO)) Will only get you those mappings where the seed_status is 100%, which is why you get many fewer results from this. But if you do this instead: res = select(hom.Hs.inp.db, keys(hom.Hs.inp.db,keytype="SCHIZOSACCHAROMYCES_POMBE"), cols="HOMO_SAPIENS", keytype="SCHIZOSACCHAROMYCES_POMBE") dim(res) This interface will you get everything (regardless of what it's score was or wasn't). If neither of these approaches is what you wanted, you can also query the DB under the hood which also has the seed_status and score for each match. Marc On 11/21/2012 07:10 PM, Rachel [guest] wrote: > I found no of homology pairs in R homology package is different from http://inparanoid.sbc.su.se/download/current/table_stats/ > > For example, there are 1804 homo-sapien-Spombe pairs in Hom.Hs.inp.db, inparanoid website claims, > > 5615 sequences H.sapiens.fa have homologs in dataset S.pombe.fa > 2986 sequences S.pombe.fa have homologs in dataset H.sapiens.fa > > > May I know did you apply any cutoff for the homology pairs in R package? > > > -- output of sessionInfo(): > > .. > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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