[Bioc-devel] do SummarizedExperiments really need colnames?

Aaron Lun alun at wehi.edu.au
Sat Dec 5 21:50:26 CET 2015

Option (2) sounds nice. Even if you used (3), I would end up naming most 
of my columns by seq_len anyway. I usually don't have very good 
candidates for column names for my counting functions; the inputs to the 
functions are BAM/other file paths that can get quite long, and I don't 
like having spaced-out columns when I look at my assays.

I concede that the example of se[,2] <- se[,1] wasn't the most 
realistic; it came about from some unit tests I was using to check 
subset replacement behaviour, and it was failing once I threw in column 

On 05/12/15 18:35, Morgan, Martin wrote:
> The philosophy motivating the check is that names make the relationship between samples and data explicit, rather than relying on fragile positional information. With this in mind, I wonder why your upstream work flow does not include dimnames on the matrix?
> That said, the check was introduced in
> ------------------------------------------------------------------------
> r68053 | mtmorgan at fhcrc.org | 2012-07-27 03:35:55 -0400 (Fri, 27 Jul 2012) | 2 lines
> SummarizedExperiment uses rowData=GRangesList() as defult
> ------------------------------------------------------------------------
> To the observations you mention below one could also add that the rownames() can be NULL, so there is an uncomfortable asymmetry.
> I could (1) remove the check (but use the DataFrame() constructor in an admittedly hackish way, not wanting to rely on the internal new() function). I could also (2) construct row / column names as seq_len(nrow()) / seq_len(ncol()).
> Or (3) the code could be tightened to more closely adhere to the philosophy above (for instance, I think duplication of columns implied by se[,2] = se[,1] is worth stop()ing over, and allowing colnames(se) = NULL only enables bad practice). Likely this would be disruptive.
> For what it's worth, we have
>> library(Biobase)
>> eset = ExpressionSet(matrix(0, 1, 2))
>> dimnames(eset)
> [[1]]
> [1] "1"
> [[2]]
> [1] "1" "2"
>> colnames(eset) = NULL
> Error in `sampleNames<-`(`*tmp*`, value = NULL) :
>    'value' length (0) must equal sample number in AssayData (2)
> so dimnames are being imposed.
> (2) would be my current compromise preference.
> Martin
> ________________________________________
> From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Aaron Lun [alun at wehi.edu.au]
> Sent: Saturday, December 05, 2015 7:36 AM
> To: bioc-devel
> Subject: Re: [Bioc-devel] do SummarizedExperiments really need colnames?
> Hello all,
> At the start of the SummarizedExperiment constructor, there's a code
> block that throws an error if 'colData' is not specified and the assay
> matrices don't have column names.
> Is this really necessary? In many cases, I just want to get a matrix
> into the SE0 object without having to worry about column names. It
> doesn't seem like there's a requirement for this in the SE0 class,
> either; it seems happy with 'colnames(se0) <- NULL', and setting
> 'colData' to a 'DataFrame' with 'NULL' row names doesn't break the
> constructor.
> The requirement for column names causes issues for some manipulations -
> for example:
> out <- SummarizedExperiment(matrix(0, 10, 5),
> colData=DataFrame(row.names=1:5))
> out[,1] <- out[,2]
> ## Error in `rownames<-`(`*tmp*`, value = c("2", "2", "3", "4", "5")) :
> ##  duplicate rownames not allowed
> While this is fair enough, it's a bit annoying if I didn't want or need
> the names in the first place.
> The error mentioned above precedes the construction of the missing
> 'colData', so if column names are missing, then a more general way to
> construct the 'colData' would to do 'new("DataFrame", nrows=ncol(assays))'.
> Cheers,
> Aaron
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