[BioC] hgu133aMAP2PROBE...fixed!

Dario Greco dario.greco at helsinki.fi
Tue Dec 13 13:28:03 CET 2005

hi everybody,
thanks a lot for all the useful information you have kindly provided.
here is how i have fixed the problem using most of the info you have provided:

> temp <- eapply(hgu133aMAP, paste, sep = "", collapse = ";")
> temp <- cbind(names(temp), unlist(temp))
> temp <- AnnBuilder:::getReverseMapping(temp)
> map2Probe <- cbind(names(temp), unlist(temp))
# (as kindly suggested by John Zhang).
# this returns map2Probe which is a matrix of dimension 2512x2 with cytobande 
name in column 1 and probesetIDs in column2.

> library(graph)
> h<-hashtable()
#i have created a hash table using hashtable() from the library(graph).

> for (i in 1:2512) 
> h[[map2Probe[i,1]]]<-unlist(strsplit(map2Probe[i,2], "\\;"))

#this populate the hash table with each element of the matrix map2Probe using 
the element in column 1 as "key" and the element in column "2" as 
"value" ("key" and "value" are from Perl terminology) and splits the "value" 
string substituting the ";" between each probesetID.

i am sure there are nicer and quicker ways, but anyway, i hope this can be 
useful to someone in the future.

thanks again,


Dario Greco

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