[Bioc-devel] Some suggestion DEXSeq

[Steve Lianoglou]

Hi,

=== 1: set rownames() on the countData object in `newExonCountSet` ===
I've built my own ExonCountSet by stitching the required pieces
together for a successful call to `newExonCountSet`.

Everything has been fine and dandy up until a call to
`estimatelog2FoldChanges`. At some point during its run, I am greeted
with:

Error in toadd[rownames(alleffects), colnames(alleffects)] <- alleffects :
  subscript out of bounds

So I've been stepping through this function to debug and I realize
that the problem is that my original `countData` matrix I passed into
`newExonCountSet` didn't have its rownames set, and it appears that
w/in the `estimatelog2FoldChanges` function, you expect it to via a
call to:

rownames(toadd) <- featureNames(ecs)

So, would it be a good idea to add some code in `newExonCountSet` to
fix this from the get go? Eg. if `is.null(rownames(countData))`, then
`rownames(countData) <- paste(geneIDs, exonIDs, sep=":")`

And add a check in the validity function for an ExonCountSet that
ensures `all(rownames(countData) == paste(geneIDs, exonIDs, sep=":"))`

=== 2: Guard against user error in exon ID names ===

As I constructed my ExounCountSet, I made a mistake in my `exonIDs`
that took me a while to figure out. I essentially did A Dumb Thing
(tm) and somehow magically had some duplicate exonIDs for the same
geneIDs.

Perhaps another check in ExonCountSet validity function to ensure that:

`all(tapply(eid, gid, function(x) length(x) == length(unique(x))))`

Thanks,
-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