On a related note to BLAST (which we've implemented an R interface for, hopefully we'll release it as part of a package by the summer's end), has anyone done any work with snarfing GEO datasets into R? I know they look a bit free-form, but it looks like about 75% (or all) of the work could be automated with a bit of work? best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M-W: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my friday location is usually completely unpredictable.)

in package annotate there is GEOAnno, a first pass at this application for GEO annotation of platforms arguments are platform (a string that identifies the platform in the GEO catalog) massageStruct (a list with elements keepIndsExpr, ncols, header, pad, stripCols -- self explanatory? the idea is that they give you a ragged table, you can find the regimented subtable (with common column number ncols) in rows given by keepIndsExpr), state the header titles you want, and do something with "," as last token and omit columns you don't need) inURL (where do you go to look at GEO datasets) the massage struct is the diciest part, but examples exist for GPL80 (HUGeneFL) and GPL91 (U95A) -- all in the annotate package under GEOAnno -- --- Vince Carey, PhD Ass't Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc@channing.harvard.edu -----BEGIN PGP PUBLIC KEY BLOCK----- Version: PGP 6.5.8 mQCNAzqIeGUAAAEEAMJXU941vIornTS52rl6z7eo+A7wwB0km/idLnkxzIhc1uLi Qtn19OyOfG6IDSucLrtmpvwagemAnQ9jL6TVDrmlrKnqsh+FFtvUuZ37eV85L70E BsS8RZCmMYHJKfrpCwegbTVZrEkd1ByquLIN/yUwxU4IcVuHxbNQk69riQ8tAAUR tBVWaW5jZW50IEouIENhcmV5LCBKci6JAJUDBRA6iHhls1CTr2uJDy0BAdsLA/wM cCzEDsP9MqodKZfDI1s/gXW6BcCuQ6n7MdEplLgmWvyqfbvRYx4upYZ3pNp8L0zU MrlR6eCTs/eDtMO/ZbGvkqqiQO6wS2fZb1T5L/DhhtT4mEAHt0E8dNBVCj+lKr3W vYS5GqO9gY4CiT3JXFH9N19pSbUQFiNDqpmG6EbWng== =DQNF -----END PGP PUBLIC KEY BLOCK-----