[BioC] error retrieving normalized probe values from "pm" array

[Lana Schaffer]

Greetings,
R version 2.7.0 (2008-04-22) 
i386-pc-mingw32 
I am retrieving the probe indexes using the indexProbes function
for each of the gene names.
    nbatch <- normalize.AffyBatch.quantiles(abatch,type="pmonly")
    gn <- geneNames(nbatch)
    gene_indexes <- indexProbes(nbatch, which="pm", genenames=gn)
I found that I need to cast the indexes as.character to retrieve
the normalized pm values.
    log2(pm(nbatch)[as.character(gene_indexes[[i]]),])
Actually I am using an lapply function:
    LG <- function(x, ma) {
     return(log2(ma[as.character(x),]))  }
    LIGC <- lapply(Rpm , LG, ma=pm(nbatch))
This worked until I ran into an error at index=100000 because it was
converted to "1e+05" and 
    log2(pm(nbatch)[as.character(gene_indexes[[374]]),])
    Error: subscript out of bounds
> as.character(gene_indexes[[374]])
 [1] "24439"  "3897"   "1e+05"  "29082"  "53595"  "53100"  "65653"
"13262" 
 [9] "45563"  "29747"  "29735"  "105476" "46438"  "83596"  "23127"
"36490" 
[17] "105458" "16956"  "98869"  "74954"  "23587" 

Can someone suggest something get me thru this problem?
Thanks,

Lana Schaffer
Biostatistics/Informatics
The Scripps Research Institute
DNA Array Core Facility
La Jolla, CA 92037
(858) 784-2263
(858) 784-2994
schaffer at scripps.edu