[BioC] Unique probes on all human affy chips
S Peri
biocperi at yahoo.com
Sun Sep 19 17:53:26 CEST 2004
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 at 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 at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
>
>
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