Replies: 6 comments
-
Also see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5240259/ |
Beta Was this translation helpful? Give feedback.
-
"Another disadvantage is that *MultiAssayExperiment* is being developed by
a large number of contributors making package improvements slow and
tedious."
thank you very much
…On Mon, Jan 30, 2017 at 3:19 PM, Aedin Culhane ***@***.***> wrote:
Also see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5240259/
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<https://github.com/waldronlab/MultiAssayExperiment/issues/165#issuecomment-276178161>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AEaOwp9dw3YPlShTBkZDUUG83VrdAXA6ks5rXkXHgaJpZM4KqWGx>
.
|
Beta Was this translation helpful? Give feedback.
-
So let's figure out what they did which is good and what is less good.
Best,
Kasper
On Mon, Jan 30, 2017 at 4:27 PM, Vince Carey <[email protected]>
wrote:
… "Another disadvantage is that *MultiAssayExperiment* is being developed by
a large number of contributors making package improvements slow and
tedious."
thank you very much
On Mon, Jan 30, 2017 at 3:19 PM, Aedin Culhane ***@***.***>
wrote:
> Also see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5240259/
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/waldronlab/MultiAssayExperiment/issues/
165#issuecomment-276178161>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/
AEaOwp9dw3YPlShTBkZDUUG83VrdAXA6ks5rXkXHgaJpZM4KqWGx>
> .
>
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<https://github.com/waldronlab/MultiAssayExperiment/issues/165#issuecomment-276196089>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AEuhn1rnNcafH5uNlvWtBau_W3f6ZfpYks5rXlW9gaJpZM4KqWGx>
.
|
Beta Was this translation helpful? Give feedback.
-
My 2 cents about what kind of extra features I would be looking for:
|
Beta Was this translation helpful? Give feedback.
-
Hi
1). easy basic filtering, eg remove rows/cols or row/cols with many
missing values, or zeros... , easy basic transformation log2/log10 . I
think this which and I know there is an easier solution
exprs(experiments(ovMAEO)[[1]])<-log2(assay(experiments(ovMAEO)[[1]]))
3) identical, setdiff, intersection a%in% x,y,z across all rows/cols
4) multi-version of summary, give the range min/max/mean/median etc of
each experiment,
5. Exploration visualization of MAE data.. shiny
finally.. its only as useful as how many people use, it... lets make it
as easy as possible for people to use, there are a few place where the
help files could have more examples
Aedin
…On 2/2/17 12:57, Laurent Gatto wrote:
My 2 cents about what kind of /extra/ features I would be looking for:
* scalability: does the architecture and the manipulation scale to
100s-1000s of samples, each with several assays
* different back-ends: local files, remote files, databases,
/in-the-cloud/ data, ... (relates to point above)
* sparse data shouldn't be an issue, or should be easy to filter out
* integration with good annotation: query using a gene name will
translate to regions or transcript/protein identifiers according
to the type of assay (I remember one of the early vignettes that
@vjcitn <https://github.com/vjcitn> had but together that really
impressed me doing queries along these lines, but I don't remember
exactly what it did).
* how easy is it to share the multi-assay data with collaborators,
in particular experimentalists (for example through shiny apps)
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<https://github.com/waldronlab/MultiAssayExperiment/issues/165#issuecomment-277032476>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AArmU-JFiP6ZUmFr-DCMuEjWUywzCW66ks5rYhkHgaJpZM4KqWGx>.
--
Aedin Culhane
---------------
Department of Biostatistics and Computational Biology,Dana-Farber Cancer Institute
Department of Biostatistics, Harvard TH Chan School of Public Health
phone: 617 640 8107
email: [email protected]
|
Beta Was this translation helpful? Give feedback.
-
Converted to discussion, just so participants know the issue wasn't just closed. |
Beta Was this translation helpful? Give feedback.
-
Just for communicating about interesting papers related to multiassay experiments.
http://onlinelibrary.wiley.com/doi/10.1002/psp4.12107/full
Beta Was this translation helpful? Give feedback.
All reactions