[BioC] getting the pm and mm indices

Donna Toleno toleno at usc.edu
Wed Nov 21 18:42:13 CET 2007


Hello Bioconductor list,

I am using the  "hgu133plus2cdf" as my cdfpackagename
and I notice that I have a problem with the following commands when a probe name is nested within other probenames. 

There is a probe named   "1053_at"  and   "241053_at"

For example, 

> a <- get("1053_at", env=get(cdfpackagename))
> a
pm mm 
NA NA 


> indexProbes(mydata, "pm")["1053_at"]
$`1053_at`
pm mm 
NA NA 

> indexProbes(mydata, "pm")["1007_s_at"]
$`1007_s_at`
 [1]  369707  563318 1049349  238813 1140401 1130782 1144961  207148 1144717  285805 1351879 1170814  906807
[14]  547053 1221909   2761

is the getProbeDataAffy a potential solution?



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