[Bioc-devel] Bug in frmaTools

[Ryan C. Thompson]

I also discovered another apparent bug later in the same function. The 
second to last line of makeVectorsAffyBatch is

     vers <- ifelse(!is.null(cdfname), 
as.character(packageVersion(cdfname)), "")

If cdfname is NULL, this line will throw an error because the second 
argument to ifelse will have length zero and "ifelse" does NOT do lazy 
evaluation.

On 07/06/2015 12:21 PM, Ryan C. Thompson wrote:
> Hello,
>
> I just encountered a bug in frmaTools that makes it impossible to use 
> on certain array platforms. The following lines in 
> makeVectorsAffyBatch fail on an AffyBatch object on the hthgu133pluspm 
> platform:
>
>     pms <- pm(object)
>     pns <- probeNames(object)
>     pmi <- unlist(pmindex(object))
>     if (!identical(as.character(pmi), rownames(pms)))
>         stop("Mismatch between pmindex and rownames of pms")
>
> I isolated the problem to five probes:
>
> > i <- which(as.character(pmi) != rownames(pms))
> > pmi[i]
>  1564498_PM_at9 205398_PM_s_at8 217695_PM_x_at7 223446_PM_s_at7 
> 237802_PM_at3
>           3e+05           5e+05           2e+05 1e+05 4e+05
> > rownames(pms)[i]
> [1] "300000" "500000" "200000" "100000" "400000"
> > as.character(pmi)[i]
> [1] "3e+05" "5e+05" "2e+05" "1e+05" "4e+05"
>
> As you can see, the problem is that as.character will happily use 
> scientific notation when it feels like it, which then fails a test for 
> string equality. I believe the solution is to replace that test with:
>
> all(sprintf("%i", pmi) == rownames(pms))
>
> -Ryan