[Bioc-devel] Bug in DEXSeq, me thinks

Dear Steve,

Thanks for the bug reports! ?I think what was missing in in the muhats
lapply was the "simplify =FALSE", what I find strange its that you are the
first one to get an error from it, might be because there is at least one
"try-error" in almost the datasets and this avoids it to be converted in a
matrix. ?Anyway I changed everything to lapply just to be on the safe side.

Regarding the:


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


I did not manage to reproduce this error, but I agree that this function
(divideWork) was a bit messy. ?With Wolfgang's help we re-engineered this
function and took away the sapply-s, I am hoping that this won't give errors
anymore. Let me know!

Thanks again!
Alejandro

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