[BioC] Unique probes on all human affy chips

[S Peri]

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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