[BioC] Unique probes on all human affy chips

Laurent Gautier lgautier at altern.org
Mon Sep 20 05:33:29 CEST 2004


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
>



More information about the Bioconductor mailing list