Thank you all very much!
Jesper
On Wed, Apr 1, 2015 at 9:54 PM, Martin Morgan mtmor...@fredhutch.org
wrote:
On 04/01/2015 07:07 AM, Martin Morgan wrote:
On 04/01/2015 05:08 AM, Michael Lawrence wrote:
It would be nice if someone from Seattle would weigh in on this.
I was hoping to weigh
It would be nice if someone from Seattle would weigh in on this.
Also, we might want to consider an assayMatrix() accessor that always
returns an assay in 2D, except, as you suggest, it might be a matrix of
multiples (vectors, matrices, etc) by putting dimensions on a list. That
way, generic code
On 04/01/2015 05:08 AM, Michael Lawrence wrote:
It would be nice if someone from Seattle would weigh in on this.
I was hoping to weigh in with 'it's done' but will instead with 'it will be
done'.
A second aspect of Jesper's data that took me a little by surprise and is
related to Michael's
Taken in the abstract, the tidy data argument is one for consistent data
structures that enable interoperability, which is what we have with
SummarizedExperiment. The long form or tidy data frame is an effective
general representation, but if there is additional structure in your data,
why not
Hi Michael
where would you put the “colData”-style metadata for the 3rd, 4th, … dimensions?
As an (ex-)physicists of course I like arrays, and the more dimensions the
better, but in practical work I’ve consistently been bitten by the rigidity of
such a design choice too early in a process.
One would need a long-form colData that aligns with the array.
But now I realize that's not what Jesper wants to do here, and is not how
SE is currently designed. Jesper is using the third (and now fourth)
dimension to store an additional dimension of information about the same
sample. We already
Hi!
The SummarizedExperiment class is an extremely powerful container for
biological data(thank you!), and all my thinking nowadays is just circling
around how to stuff it as effectively as possible.
Have been using 3 dimension for a long time, which has been very
successful. Now I also have a
