mypacks <- c("hgu133aprobe", "hgu95av2probe") ## put all the cdfenv ## packs you want here allmyprobes <- c() for (i in seq(along=mypacks)) { library(mypacks[i], character.only=TRUE) allmyprobes <- unique(c(get(mypacks[i])$sequence, allmyprobes)) ## memory saving... tmp <- paste("package", mypacks[i], sep=":") detach(pos=match(tmp, search())) } ## unique probe sequences are in 'allprobes'... ## ... and shouldn't take 20 hours for 13 chips... If you feel like leaving C++ aside: - To map probes to reference sequences the package 'matchprobes' can be useful. - To manipulate mappings, the package 'altcdfenvs' might have functions of interest as well. L. S Peri wrote: > Hi Laurent, > I am interested in getting individual probes. I want > to export them into my postgres table and map link > them to sequences. > Thanks > Peri. > --- Laurent Gautier <lgautier@altern.org> wrote: > > >>Peri, >> >> >>I am not certain of what you want: are they the >>probe sets >>or the individual probes ? >>If you want probe sets, I think that you could do it >>in R. The execution time would be few seconds (on >>reasonably recent >>computer...) >> >>Example: >> >>mycdfs <- c("hgu133acdf", "hgu95av2cdf") ## put all >>the cdfenv packs you >> ## want >>here >> >>allmyids <- c() >> >>for (i in seq(along=mycdf)) { >> library(mycdfs[i], character.only=TRUE) >> allmyids <- unique(c(ls(get(mycdfs[i])), >>allmyids)) >> >> ## memory saving... >> tmp <- paste("package", mycdfs[i], sep=":") >> detach(pos=match(tmp, search())) >>} >> >>## unique probe set ids are in 'allmyids'... >> >> >>If you want the probes, a variation of the code >>above should make >>it. >> >> >>Hoping it helps, >> >> >> >>L. >> >> >> >>S Peri wrote: >> >>>Dear group, >>> Is there any place where I can get all the unique >>>probe ids for all the Affy human chips (~13 >> >>chips). >> >>>I am trying to get the unique probes (no >> >>duplicates). >> >>>It turned out to be very computing intensive >> >>problem. >> >>>I took all the probes from all 13 chips and made a >>>program that writes the the unique id (if there >> >>are >> >>>duplicates, for e.g. 64474_g_at is there on >> >>HG-U95C, >> >>>HGU133, HGU133A2, and 133_plus2. In this case my >>>program will write 64474_g_at once in my output). >>>Using c++ code it is running for the last 20 hrs. >> >>I >> >>>made sure there are no bad loops that would put me >> >>in >> >>>infinite loop situation. It would be nice to have >> >>all >> >>>the uniqe ids in some place where i can use them >>>directly for my annotation purposes. >>> >>>Thanks >>>Peri. >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor@stat.math.ethz.ch >>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >> >> > > > > > _______________________________ > Do you Yahoo!? > Declare Yourself - Register online to vote today! > http://vote.yahoo.com >