[Bioc-devel] Bug in frmaTools

[Matthew McCall]

Ryan,

Thanks for pointing these out. I'll look into them soon, but I imagine your
assessment is correct.

Best,
Matt



On Mon, Jul 6, 2015 at 5:42 PM, Ryan C. Thompson <rct at thompsonclan.org>
wrote:

> 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
>>
>
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-- 
Matthew N McCall, PhD
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