[BioC] breastCancerNKI patients question

[Sean Davis]

On Tue, Oct 25, 2011 at 7:38 AM, Xavier Robin <Xavier.Robin at unige.ch> wrote:
> Hello everyone!
>
>
> According to the documentation of package breastCancerNKI, nki is a
> merge of two datastets by van’t Veer et al. and van de Vijver et al. We
> should have 117 patients for the former, and 295 for the latter, summing
> up to 412 patients.
>
> However the nki dataset contains only 337 patients:
>
>> dim(pData(nki))
> [1] 337  21
>> dim(exprs(nki))
> [1] 24481   337
>
> Apparently the "series" annotation specifies which dataset the patients
> belong to:
>
>> table(pData(nki)$series)
>
>  NKI NKI2
>  117  220
>
> So we would have all 117 patients from van’t Veer et al, but only 220 of
> the 295 patients of van de Vijver et al.
>
> Is it correct?
> * If yes, where are the 75 remaining patients?
> * If no, what did I misunderstand?

There was overlap between the van't Veer and van de Vijver datasets,
so the numbers are for unique patients only, I believe.

Sean