I have a query about the format of the organism name to use in ABPkgBuilder and getSrcUrl functions of AnnBuilder. It seems in some functions organism should be the official name (eg Mus Musculus) but in other functions it should be the common name (eg mouse). The vignette states that you can get the src URls by calling mySrcUrl <- getSrcUrl("all","mouse") However this fails for Golden Path (UCSC) Url. The fix is to use the scientific name Mus Musculus. e.g. mySrcUrl <- getSrcUrl("all","Mus Musculus") When calling the ABPkgBuilder function it states that the organism argument may only be "human", "mouse" or "rat". I assume if I use Mus Musculus in getSrcUrl and mouse in ABPkgBuilder all will be ok. This seems a little inconsistent so are there plans to accept either common or official name? I assume if I use organism = "Mus Musculus" in ABPkgBuilder it will generate an error. Cheers Chris (RH9 Linux, R 2.1.0, BioC 1.6 = AnnBuilder 1.5.31) Dr Chris Wilkinson Senior Research Officer (Bioinformatics) | ARC Research Associate Child Health Research Institute (CHRI) | Microarray Analysis Group 7th floor, Clarence Rieger Building | Room 121 Women's and Children's Hospital | School of Applied Mathematics 72 King William Rd, North Adelaide, 5006 | The University of Adelaide, 5005 Math's Office (Room 121) Ph: 8303 3714 CHRI Office (CR2 52A) Ph: 8161 6363 Christopher.Wilkinson@adelaide.edu.au http://mag.maths.adelaide.edu.au/crwilkinson.html

>I assume if I use Mus Musculus in getSrcUrl and mouse in ABPkgBuilder all will >be ok. This seems a little inconsistent so are there plans to accept either >common or official name? I assume if I use organism = "Mus Musculus" in >ABPkgBuilder it will generate an error. AnnBuilder now only takes scientific names. Please let me know if there is any function that does not comply and I will fix it. Thanks. > >Cheers >Chris > >(RH9 Linux, R 2.1.0, BioC 1.6 = AnnBuilder 1.5.31) > >Dr Chris Wilkinson > >Senior Research Officer (Bioinformatics) | ARC Research Associate >Child Health Research Institute (CHRI) | Microarray Analysis Group >7th floor, Clarence Rieger Building | Room 121 >Women's and Children's Hospital | School of Applied Mathematics >72 King William Rd, North Adelaide, 5006 | The University of Adelaide, 5005 > >Math's Office (Room 121) Ph: 8303 3714 >CHRI Office (CR2 52A) Ph: 8161 6363 > >Christopher.Wilkinson@adelaide.edu.au > >http://mag.maths.adelaide.edu.au/crwilkinson.html > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084