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List:       bioc-devel
Subject:    Re: [Bioc-devel] Some suggestion DEXSeq
From:       Steve Lianoglou <mailinglist.honeypot () gmail ! com>
Date:       2012-07-20 13:13:41
Message-ID: CAHA9McNAiviOZuXkeBhfgYYEwpdahBoQJ_f5hXBDG6LKoVvAgw () mail ! gmail ! com
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Hi Alejandro,

Thanks for the quick response.

Perhaps you might like to add your
`any(duplicated(rownames(countData)))` check to the validty function
as well, since, I guess technically that's what it is?

Or not ... up to you, obviously.

Thanks again!

-steve

On Fri, Jul 20, 2012 at 7:23 AM, Alejandro Reyes
<alejandro.reyes@embl.de> wrote:
> Hi Steve,
>
> Thanks for your email and advice, I added the next code in newExonCountSet:
>
>
> rownames(countData) <- paste(geneIDs, exonIDs, sep=":")
>
> if( any( duplicated(rownames(countData) ) ) ) {
>    stop("The geneIDs or exonIDs are not unique")
> }
>
> And in the validity function:
>
> if( ! all(featureNames(object) == paste(geneIDs(object), exonIDs(object),
> sep=":") ) )
>    return( "The featureNames do not match with the geneIDs:exonIDs" )
> if( ! all(rownames( counts(object) ) == featureNames(object) ) )
>    return( "The rownames of the count matrix do not coincide with the
> featureNames" )
> if( ! all(rownames( fData( object ) ) == featureNames( object ) ) )
>    return( "The rownames of the featureData do not coincide with the
> featureNames" )
>
> I think this would handle any possible problem!
> Thanks again,
>
> Alejandro
>
>
>
>> 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

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