For what it's worth, I've written a class which I have creatively named
SubsettableListOfArrays which basically taking the "subset everything
together" aspect of eSet and SummarizedExperiment and making it as
generic as possible. It's basically like (non-ranged)
SummarizedExperiment, except tha
While it's useful (and often necessary) to store the big matrices out of
core, it would be convenient to store the metadata (the other components of
the object) along with the matrices. Something along the lines of HDF5, but
we would want to keep things abstract. Other options include GDS (for
geno
While we are on the topic, my GenoSet class will become a subclass of
RangedSummarizedExperiment, rather than eSet, after this upcoming release.
For this release both APIs work (colnames and sampleNames, etc.)
I think the range-free SummarizedExperiment will be great. I've seen a lot
of Expression
I think the simplest course is to leave your remote as is, and not use the
Bioconductor mirror as a true remote. Instead, keep using the git-svn
bridge to push to Bioconductor. And put your github remote as the place to
submit issues, etc
Robert
On Fri, Sep 18, 2015, 5:18 PM Steffen Neumann wrot
In the dev version, SummarizedExperiment has been split into
RangedSummarizedExperiment (equivalent to the current
SummarizedExperiement, with rowRanges) and SummarizedExperiment (kind of
like eSet, no rowRanges). Given that eSet objects also support multiple
assayData elements, I believe the n
Interesting, thanks for the pointer.
In light of the existing (and future) work on this, may I suggest an eSet
like class, but build using the technologies in SummarizedExperiment. Ie.
a SummarizedExperiment without the rowRanges. I would very much like this
for modern work using eSet like conta
thanks to all, lots of potential here.
On Fri, Sep 18, 2015 at 3:28 PM, Peter Haverty
wrote:
> Yes, bigmemoryExtras::BigMatrix and genoset::RleDataFrame() are good
> tricks for reducing the size of your eSets and SummarizedExperiments. Both
> object types can go into assayData or assays. In fac
Yes, bigmemoryExtras::BigMatrix and genoset::RleDataFrame() are good tricks
for reducing the size of your eSets and SummarizedExperiments. Both object
types can go into assayData or assays. In fact, that's what they were
designed for.
At Genentech, we use these for our 2.5e6 x 1e3 rectangular dat
Hi,
sorry for asking another git question, but I want to make sure
I don't mess up. If something like this was answered elsewhere
and I missed it, just point me there.
I had developed a package up to Version 0.99.7 on github
in https://github.com/sneumann/mtbls2/ ,
and now after acceptance to
bigmemoryExtras (Peter Haverty's extensions to bigMemory/bigMatrix) can be
handy for this, as it works well as a backend, especially if you go about
splitting by chromosome as for CNV segmentation, DMR finding, etc. It's
not as seamless as one might like, but it's the closest thing I've found.
S
Hi Vince,
This is actually on "our" TODO list for after the release.
SummarizedExperiment was designed to support alternate back end
for the assays slot. More details and proof of concept are
in ?Assays.
H.
On 09/18/2015 01:29 PM, Vincent Carey wrote:
i am dealing with ~700 450k arrays
they a
i am dealing with ~700 450k arrays
they are derived from one study, so it makes sense to think of
them holistically.
both the load time and the memory consumption are not satisfactory.
has anyone worked on an object type that implements the rangedSE API but has
the assay data out of memory?
>
Thanks Jesper for your reply.
I am afraid however thats what I did before (see the details of my
original message). The real problem is the file .Rbuildignore which
causes a rebase that then finds the conflict in DESCRIPTION (and other
files as I fix that one; I guess it is trying to go too far in
Hi Diego,
I had the same problem some days ago. Can't tell if this is the right way
to solve the problem, but it worked, and this is what I did,
1) modified the file under conflict, in your case DESCRIPTION.
2) git rebase --continue
3) git rebase --skip
#This is the selected output from my bash h
Dear all,
I am now having a similar issue (see bellow) with my other package
rTRM and so would like to bring the attention to this thread again.
Anyone using git mirrors experiencing something similar and/or knowing
how to fix it? Thank you very much in advance.
Best,
Diego
On Tue, Sep 8, 2015 a
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