One more thing. See below...
On 09/13/2017 02:54 PM, Ludwig Geistlinger wrote:
Coercing vice versa, i.e. from SummarizedExperiment to ExpressionSet,
which is defined in
SummarizedExperiment/R/makeSummarizedExperimentFromExpressionSet.R
as follows:
setAs("SummarizedExperiment", "ExpressionSet"
Hi Ludwig,
Excellent catch! Thanks for the report.
This should be fixed in SummarizedExperiment release (1.6.4) and devel
(1.7.7).
Cheers,
H.
On 09/13/2017 02:54 PM, Ludwig Geistlinger wrote:
Coercing vice versa, i.e. from SummarizedExperiment to ExpressionSet,
which is defined in
Summarized
Coercing vice versa, i.e. from SummarizedExperiment to ExpressionSet,
which is defined in
SummarizedExperiment/R/makeSummarizedExperimentFromExpressionSet.R
as follows:
setAs("SummarizedExperiment", "ExpressionSet", function(from)
as(as(from, "RangedSummarizedExperiment"), "ExpressionSet")
)
I see how an eSet maps to a SummarizedExperiment; one can look at the
assays in the object. I agree with Levi/Herve that this is the natural
(correct) choice. It is less clear how you get the ranges for a
RangedSummarizedExperiment without making assumptions.
On Mon, Sep 11, 2017 at 8:09 PM, Her
I don't know the reasons behind this choice, I didn't implement
these methods. It would make sense to have these coercions defined
for the eSet,SummarizedExperiment and eSet,RangedSummarizedExperiment
signatures if they only access the eSet part of the object.
I'll look into this.
H.
On 09/11/20
Thanks Ludwig and Kasper. This old presentation from Martin also helped me
a lot:
https://www.bioconductor.org/packages/devel/bioc/vignettes/Biobase/inst/doc/BiobaseDevelopment.pdf
But I still wonder, why provide the coercion for ExpressionSet, if
providing it for eSet would work not only for Exp
An ExpressionSet is an eSet that is guaranteed to have an "exprs" assay.
That makes no sense for example for methylation where we have (say)
Green/Red assays or Meth/Unmeth assays (or transformations of these).
Best,
Kasper
On Mon, Sep 11, 2017 at 3:31 PM, Ludwig Geistlinger <
ludwig.geistlin...@
Concerning 1) Why have some developers chosen to extend eSet instead of
ExpressionSet:
As far as I understand it, ExpressionSet was thought to exclusively
represent a microarray experiment (MIAME = Minimum Information About a
Microarray Experiment).
Thus, back in the days when more and more peopl
On Mon, Sep 11, 2017 at 2:02 PM, Hervé Pagès wrote:
> Hi,
>
> I added coercion from ExpressionSet to SummarizedExperiment in
> SummarizedExperiment 1.7.6.
>
Thank you Hervé!
> The current behavior of the SummarizedExperiment() constructor
> when called on a ExpressionSet object doesn't make mu
Hi,
I added coercion from ExpressionSet to SummarizedExperiment in
SummarizedExperiment 1.7.6.
The current behavior of the SummarizedExperiment() constructor
when called on a ExpressionSet object doesn't make much sense to
me. I'd rather have it consistent with what the coercion does.
Will fix i
It's probably good keeping coercion and construction distinct,
although we have violated that recently with GRanges(). It now
attempts to coerce its first argument to a GRanges. Don't want to
derail the discussion, but it's another data point.
Michael
On Mon, Sep 11, 2017 at 9:26 AM, Levi Waldron
On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger <
ludwig.geistlin...@bio.ifi.lmu.de> wrote:
> I guess we discussed this with Davide Risso @Bioc2017 in the
> MultiAssayExperiment workshop.
>
> > SummarizedExperiment(mouseData)
>
> puts the eSet (rather counterintuitively) into `assays` of
> `S
I guess we discussed this with Davide Risso @Bioc2017 in the
MultiAssayExperiment workshop.
> SummarizedExperiment(mouseData)
puts the eSet (rather counterintuitively) into `assays` of
`SummarizedExperiment`, it does not really coerce it to
SummarizedExperiment, eg. `fData` and `pData` are not ac
Thanks Martin! I see the RangedSummarizedExperiment coercion method works
when there are no mappable ranges (for example curatedMetagenomicData
ExpressionSet objects), although the rowRanges is a GRangesList of empty
elements. It might be worth also having a SummarizedExperiment coercion
method it
On 09/10/2017 08:38 PM, Levi Waldron wrote:
I just dug up this old thread because I realized we still don't have a
coercion method as(sample.ExpressionSet, "SummarizedExperiment"). Since we
try as(sample.ExpressionSet, "RangedSummarizedExperiment"); see
?makeSummarizedExperimentFromExpressionS
I just dug up this old thread because I realized we still don't have a
coercion method as(sample.ExpressionSet, "SummarizedExperiment"). Since we
do have SummarizedExperiment(sample.ExpressionSet), could the coercion
method also be added easily?
> library(Biobase) > library(SummarizedExperiment) >
Hi,
On 09/20/2014 11:14 AM, Martin Morgan wrote:
On 09/20/2014 10:43 AM, Sean Davis wrote:
Hi, Vince.
Looks like a good start. I'd probably pull all the assays from
ExpressionSet into SummarizedExperiment as the default, avoiding data
coercion methods that are unnecessarily lossy. Also, as i
Would be very useful in epivizr. Right now we have a little bit of code
that can be made much more general:
https://github.com/epiviz/epivizr/blob/master/R/register-methods.R#L73
On Sat, Sep 20, 2014 at 5:19 PM, Michael Love
wrote:
> On Sep 20, 2014 2:15 PM, "Martin Morgan" wrote:
> >
> > On 0
On Sep 20, 2014 2:15 PM, "Martin Morgan" wrote:
>
> On 09/20/2014 10:43 AM, Sean Davis wrote:
>>
>> Hi, Vince.
>>
>> Looks like a good start. I'd probably pull all the assays from
>> ExpressionSet into SummarizedExperiment as the default, avoiding data
>> coercion methods that are unnecessarily l
On 09/20/2014 10:43 AM, Sean Davis wrote:
Hi, Vince.
Looks like a good start. I'd probably pull all the assays from
ExpressionSet into SummarizedExperiment as the default, avoiding data
coercion methods that are unnecessarily lossy. Also, as it stands, the
assayname argument is not used anyway
Hi, Vince.
Looks like a good start. I'd probably pull all the assays from
ExpressionSet into SummarizedExperiment as the default, avoiding data
coercion methods that are unnecessarily lossy. Also, as it stands, the
assayname argument is not used anyway?
Sean
On Sat, Sep 20, 2014 at 10:38 AM,
21 matches
Mail list logo
