dear maintainers of Biobase and lumi,
this is a question raised from a different thread a few days ago here:
https://stat.ethz.ch/pipermail/bioc-devel/2014-January/005129.html
the matrix of genes by samples expression values in an 'ExpressionSet'
object can be accessed and replaced with the
On 01/10/2014 12:07 AM, Maintainer wrote:
dear maintainers of Biobase and lumi,
this is a question raised from a different thread a few days ago here:
https://stat.ethz.ch/pipermail/bioc-devel/2014-January/005129.html
the matrix of genes by samples expression values in an 'ExpressionSet'
Unfortunately, you may want to be careful about making it too robust
(depending on what you mean). For example filtering methods could very
well be seen as replacing one matrix with a smaller one. Not sure if these
methods use exprs-, but that is probably how I would do it.
What would be better
hi Martin,
along the lines of the situation that Kasper describes, my use case is
that GSVA transforms a matrix of expression values of genes-by-samples
into a matrix of summary expression values of pathways-by-samples. When
the input is an 'ExpressionSet' object, GSVA simply does something
Robert: The alternative to using exprs- is to instantiate a new object,
just copying the old phenodata.
Kasper
On Fri, Jan 10, 2014 at 10:58 AM, Levi Waldron levi.wald...@hunter.cuny.edu
wrote:
On Fri, Jan 10, 2014 at 9:59 AM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
hi Kasper,
you're right. i should have done this upfront, this was too much S4
magic to be true :)
cheers,
robert.
On 1/10/14 5:14 PM, Kasper Daniel Hansen wrote:
Robert: The alternative to using exprs- is to instantiate a new object,
just copying the old phenodata.
Kasper
On Fri, Jan
No Robert, in my opinion you did the right thing. You're right to expect
the replacement operation to do the right thing and it is a bug that it
doesn't work.
Kasper
On Fri, Jan 10, 2014 at 4:58 PM, Robert Castelo robert.cast...@upf.eduwrote:
hi Kasper,
you're right. i should have done
