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

[Benilton Carvalho]

Thank you very much, Martin.

b

On 11 June 2012 22:03, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793