[Bioc-devel] list() as dimnames in assayDataNew

[Martin Morgan]

On 06/11/2012 04:42 AM, Benilton Carvalho wrote:
> Hi,
>
> Biobase::assayDataNew() now assigns list() as dimnames(elt) if the
> original dimnames(elt) is NULL.
>
> This is a consequence of
>
> dimnames(elt)<- lapply(dimnames(elt), unname)
>
> because lapply(NULL, unname) is list().
>
> Although this works fine for regular R objects (because list() is
> coerced back to NULL), this fails when elt is an ff object.
>
> library(ff)
> library(Biobase)
> x = matrix(1:4, 2)
> y = as.ff(x)
> dimnames(x)
> dimnames(y)
> assayDataNew(exprs=x)
> assayDataNew(exprs=y)
>
> The documentation for dimnames()<- value states that value "can be
> NULL or a list of the same length as dim(x). If a list, its components
> are either NULL or a character vector with positive length of
> appropriate dimension of x."
>
> Following the strict definition of value given in the documentation
> (therefore, ignoring the coercion described in Details), would you
> guys consider replacing
>
>          dimnames(elt)<- lapply(dimnames(elt), unname)
>
> by
>
>          dimnames(elt)<- ifelse(is.null(dimnames(elt)), NULL,
> lapply(dimnames(elt), unname))
>
> ?

Hi Benilton -- I did

   if (!is.null(dimnames(elt)))
       dimnames(elt) <- lapply(dimnames(elt), unname)

in 2.17.6. Thanks for the report.

Martin

>
> Thank you very much,
>
> benilton
>
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