Re: [Bioc-devel] EXTERNAL: Re: name of git repo for brgedata/BRGEdata package

[Shepherd, Lori]

It seems you have submitted a bad id and key to the form.

1. For GitHub ID, it needs to submit  as `carleshf`, not `github.com/carleshf`.

2. the SSH key needs the `ssh-rsa` header in front of the key. It was submitted 
without it.

Please resubmit.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Turaga, Nitesh
Sent: Tuesday, October 24, 2017 9:34:15 AM
To: Shepherd, Lori
Cc: bioc-devel@r-project.org
Subject: Fwd: EXTERNAL: Re: name of git repo for brgedata/BRGEdata package



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From: Carles Hern�ndez 
Sent: Tuesday, October 24, 2017 9:11:30 AM
To: Turaga, Nitesh
Cc: Juan Ram�n Gonzalez; Carlos Ruiz; Ramos Perez, Marcel; Morgan, Martin; Van 
Twisk, Daniel; Herv� Pag�s
Subject: EXTERNAL: Re: name of git repo for brgedata/BRGEdata package

Dear Nitesh,


I checked again if I can fetch the repo in order to push the properly changes 
to "brgedata" (and to "omicRexposome"). As you can see:

chernandez@workstation01 MINGW64 ~/Projects/BRGEdata (master)
$ git fetch --all
Fetching origin
Fetching upstream
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream


Kind regards,

Carles Hernandez-Ferrer
Bioinformatic Analyst / PhD Student
ISGlobal
Barcelona Institute for Global Health - Campus Mar
Barcelona Biomedical Research Park (PRBB) (office 183.01 A)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 73 22
carles.hernan...@isglobal.org
www.isglobal.org | 
www.carleshf.com

We are pleased to tell you that after three years of a strategic alliance 
between ISGlobal and CREAL, both institutions have merged. The resulting 
institution, which retains the ISGlobal name, will build upon the existing 
areas of excellence to become a world-class player in research, education and 
innovation in Global Health. More info at http://ow.ly/krQd301Nj3w

On 21 October 2017 at 19:23, Herv� Pag�s 
> wrote:
Thanks Carles for the update.

Please do "Reply All" on further communications. Thanks!

Regards,
H.


On 10/21/2017 12:50 AM, Carles Hern�ndez wrote:
Dear Herv�,


Yesterday I connacted Nitesh because it seems that I have some permision
problems with my user. We keep in mind that we msut solve this as fast
as possible.


Kidnr egards,

Carles Hernandez-Ferrer
Bioinformatic Analyst / PhD Student
*ISGlobal*
Barcelona Institute for Global Health - Campus Mar
Barcelona Biomedical Research Park (PRBB) (office 183.01 A)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 73 22
carles.hernan...@isglobal.org 
>
www.isglobal.org

| www.carleshf.com

/
//We are pleased to tell you that after three years of a strategic
alliance between ISGlobal and CREAL, both institutions have merged. The
resulting institution, which retains the ISGlobal name, will build upon
the existing areas of excellence to become a world-class player in
research, education and innovation in Global Health. More info at
http://ow.ly/krQd301Nj3w
/

On 21 October 2017 at 09:02, Herv� Pag�s 

>> wrote:

Hi omicRexposome/BRGEdata developers,

When the BRGEdata package was accepted, we added the brgedata git
repo to the Bioconductor git server:

https://git.bioconductor.org/packages/brgedata



Unfortunately at the time we did this, the name of the git repo didn't

Re: [Bioc-devel] Modeling (statistic, p-value) pairs in MultiAssayExperiment

[Francesco Napolitano]

Thank you!

Fig 1 shows the pipeline for a single database of pathways, but we
used 10 different databases (GO, KEGG, Reactome...). Currently we use
all of MSigDB, which includes 24 subcategories, and we have a matrix
of ES and a matrix of pvalues for each. You always have the same drugs
over columns, but different pathways over rows. Keeping them separated
is necessary (you don't want to rank pathways across unrelated
databases). On the other hand, if I build one SummarizedExperiment for
each database, I have to replicate the common metadata across all of
them, and also lose most of the features that going through the burden
of modeling my data with SE were all about :-/.

Note I'm considering all this for a package under review to possibly
improve its interoperability with existing packages.


On Tue, Oct 24, 2017 at 2:45 PM, Levi Waldron
 wrote:
> On Oct 24, 2017 6:14 AM, "Francesco Napolitano"  wrote:
>
> I'm converting gene expression profiles to "pathway expression
> profiles" (https://doi.org/10.1093/bioinformatics/btv536), so for each
> pathway I have an enrichment score and a p-value. I guess it would be
> like modeling gene expression data where limma-like preprocessing was
> performed, so you have a fold change - p-value pair for each gene.
> Isn't there a data model for that?
>
>
> Nice paper, thanks for the link! Could you explain the problem a little more
> using the terminology of your paper? I see your enrichment values matrix
> (fig 1c ESij) of pathways x cell lines, and imagine additional associated
> matrices of p-values and ranks, but where do assays with different rows come
> in?
>

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Re: [Bioc-devel] EXTERNAL: Permission denied (publickey) while pushing changes to Github

[Turaga, Nitesh]

Hi 

Your key should have access now. Please try again. 

Best,

Nitesh 

> On Oct 24, 2017, at 7:01 AM, Sokratis Kariotis  
> wrote:
> 
> Hey all, I am trying to push som changes to my newly accepted packages
> (pcxn,pcxnData) and get this:
> 
> ''Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.''
> 
> If it helps my 'git remote -v' results are the following:
> 
> origin  https://github.com/hidelab/pcxnData.git (fetch)
> origin  https://github.com/hidelab/pcxnData.git (push)
> upstreamg...@git.bioconductor.org:packages/pcxnData.git (fetch)
> upstreamg...@git.bioconductor.org:packages/pcxnData.git (push)
> 
> Thanks in advance!
> -- 
> Sokratis Kariotis
> Scientific Programmer
> Hidelab
> Sheffield Institute for Translational Neuroscience
> 385a Glossop Rd, Sheffield, S10 2HQ
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] "extra" unit tests

[Peter Hickey]

A partial answer if you are using the 'testthat' framework: you can use
`testthat::skip_on_bioc()` to specify that a test should be skipped if it
is running on the BioC build machines. The test will otherwise be run
(e.g., during local development). There are some other `testthat::skip*()`
functions that may also be useful.
Cheers,
Pete

On Wed, 25 Oct 2017 at 12:47 Levi Waldron 
wrote:

> Any thoughts about how to implement optional or "extra" unit tests, that
> are too resource intensive to be part of the Bioconductor daily builds, but
> that should be run once in a while, say with major updates?
>
> [[alternative HTML version deleted]]
>
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>

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Re: [Bioc-devel] "extra" unit tests

[Levi Waldron]

Thanks Pete! Didn't know about those.

On Oct 24, 2017 11:17 PM, "Peter Hickey"  wrote:

> A partial answer if you are using the 'testthat' framework: you can use
> `testthat::skip_on_bioc()` to specify that a test should be skipped if it
> is running on the BioC build machines. The test will otherwise be run
> (e.g., during local development). There are some other `testthat::skip*()`
> functions that may also be useful.
> Cheers,
> Pete
>
> On Wed, 25 Oct 2017 at 12:47 Levi Waldron 
> wrote:
>
>> Any thoughts about how to implement optional or "extra" unit tests, that
>> are too resource intensive to be part of the Bioconductor daily builds,
>> but
>> that should be run once in a while, say with major updates?
>>
>> [[alternative HTML version deleted]]
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

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