[Bioc-devel] Bug in DEXSeq, me thinks

[Steve Lianoglou]

And another sapply -> lapply in divideWork (core_functions ~ line 496):

fData(ecs)[,fattr][rows] <- do.call(c, sapply(...))

is exploding when

length(testablegenes) %% mc.cores == 0

-steve

On Tue, Mar 13, 2012 at 5:33 AM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> And while we're at it, I think there's another place you need to swap
> out an lapply for an sapply (or set simplify=FALSE) in the
> `divideWork` function.
>
> Specifically, it seems that when `testablegenes` is divisible by mc.cores:
>
> (1) This sapply call returns a matrix back to `rowlist`, when you
> really want a list, since you will `do.call(c, rowlist)` later:
>
> rowlist <- sapply(1:mc.cores, function(i){which(fData(ecs)$geneID %in%
> subgenes[[i]])})
>
> (2) Ditto for your `stopifnot` check. The `do.call(c, sapply(...))`
> explodes because the sapply returns a matrix:
>
> stopifnot(all(as.character(fData(ecs)$geneID)[rows] == do.call(c,
> sapply(allecs, function(x){as.character(fData(x)$geneID)}))))
>
> ... or ... at least these things are happening for me right now.
>
> I have a weird feeling that I might have hosed something, since I
> reckon people would have tripped over this by now since it's easy to
> fall into this scenario where:
>
> length(testablegenes) %% mc.cores == 0
>
> when mc.cores == 2
>
> So ... hopefully I'm not just chasing my tail then asking you to chase yours.
>
> Thanks,
> -steve
>
>
>
>
> On Tue, Mar 13, 2012 at 5:10 AM, Steve Lianoglou
> <mailinglist.honeypot at gmail.com> wrote:
>> And then add names back to muhats, of course:
>>
>> On Mon, Mar 12, 2012 at 8:32 PM, Steve Lianoglou
>> <mailinglist.honeypot at gmail.com> wrote:
>>> Hi,
>>>
>>> It just so happened that DEXSeq, for reasons I couldn't explain, kept
>>> throwing errors during a call to `estimateDispersions`. I couldn't
>>> explain it because I really thought I didn't change much, but I've got
>>> some magic combination of samples I'm currently trying to
>>> estimateDispersion on that none of them throw any errors while
>>> estimate `muhats` (line 245 of core_functions.R):
>>>
>>> muhats <- sapply(testablegenes, function(gn) {
>>> ...
>>> muhat
>>> })
>> [snip]
>>
>> names(muhats) <- testablegenes
>>
>> -steve
>> --
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>>  | Memorial Sloan-Kettering Cancer Center
>>  | Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact