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

Hi, thanks for the suggestion. The point is that I have multiple assays, each of which is made of statistic-p-value pairs. Within each assay, the two matrices have of course same rows and columns, but different assays will have different rows (same columns). So I should flatten everything and mode

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

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

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

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' resu

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

Just realized my answer yesterday went to Francesco and not the list: Since it sounds like you have two matrices of the same dimensions, why not represent these as two assays in a SummarizedExperiment? E.g.: > statvals <- matrix(rnorm(100), ncol=5) > pvals <- pnorm(statvals) > library(Summarized

[Bioc-devel] Shields/Badges on Package landing pages

There have been a number of issues with the shields/badges on the package landing pages do to the Bioconductor git transition. We are in the process of updating the procedure to generate these shields to correct out-of-date or missing items. We are disabling the affected shields/badges so they

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

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 whe

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

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 colum

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

Get Outlook for Android 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:

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

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

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

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

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

It works now, thank you for your timely fix! On 24 October 2017 at 15:54, Turaga, Nitesh wrote: > Hi > > Your key should have access now. Please try again. > > Best, > > Nitesh > > > On Oct 24, 2017, at 7:01 AM, Sokratis Kariotis < > s.kario...@sheffield.ac.uk> wrote: > > > > Hey all, I am tryin

Re: [Bioc-devel] Shields/Badges on Package landing pages

Yes I am in the process of updating that one as we speak - It hopefully should be active tomorrow. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Bioc-devel] EXTERNAL: R version dependence of a new package

Dear Yaoyong, Can you remove the R version dependency from your DESCRIPTION file entirely? That will eliminate the warning, but will also not suggest to users that they need a newer version of R than is necessary. R 2.3.0 was released in 2006, so it seems highly unlikely that anyone would be

[Bioc-devel] Problem with the MAC build machine

Hi All I am the maintainer of cellbaseR, a client for the CellBase webservices Is a problem with the MAC build machine It has been giving me TIMEOUT errors for a while now, while the build progresses normally in the Linux and Windows machines Best regards [[alternative HTML version delet

Re: [Bioc-devel] Help with a Gviz-plot that differs on a Mac and on an Ubuntu machine

Thank you for testing, Dario! There seems to be something wrong with those 5' and 3' markers. I'll look into it, thanks! On Mon, Oct 23, 2017 at 3:00 AM, Dario Strbenac wrote: > Good day, > > I can't reproduce the problem on Windows, so it seems specific to MacOS. > > Is having 5' and 3' labels

[Bioc-devel] Install directly from the bioconductor git repo?

Can I install a package directly from a Bioconductor git repository? Like I can for example using devtools and a github repository like this: `install_git("git://github.com/hadley/stringr.git")`? What would be the link for a Bioconductor package? Also, can I link directly to a source code file som

[Bioc-devel] Build warnings for missing documentation on defunct functions

Dear Bioconductor maintainers, The build report for our package 'MutationalPatterns' signals a warning for functions that are deprecated. I explicitly added "@noRd" to the function header to prevent it from ending up in the documentation. How should I go about fixing this warning? The other

Re: [Bioc-devel] Problem with the MAC build machine

On a similar note, I'm the maintainer of the trena package. I've been getting TIMEOUT on the Windows platform, but the build progresses on Linux and Mac. I'm hoping this doesn't adversely affect the package's inclusion in 3.6 On Tue, Oct 24, 2017 at 12:15 PM, mohammed Elsiddieg wrote: > Hi All >

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

OK, I think I'm understanding better now. The best immediate solution that I can think of is a SummarizedExperiment for each signatures database, then pasting those SummarizedExperiments together with a MultiAssayExperiment. Something like this: set.seed(1) statvals <- matrix(rnorm(100), ncol=5) r

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

On Mon, Oct 23, 2017 at 9:15 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > Are you discussing statistics of the same dimension as the data (unusual) > or summary statistics? We should think about a MAE version of summary > statistics, but that is not captured in current represe

Re: [Bioc-devel] Install directly from the bioconductor git repo?

On 10/24/2017 04:16 PM, Stian Lågstad wrote: Can I install a package directly from a Bioconductor git repository? Like I can for example using devtools and a github repository like this: `install_git("git://github.com/hadley/stringr.git")`? What would be the link for a Bioconductor package? ins

Re: [Bioc-devel] Problem with the MAC build machine

On 10/24/2017 03:15 PM, mohammed Elsiddieg wrote: Hi All I am the maintainer of cellbaseR, a client for the CellBase webservices Is a problem with the MAC build machine It has been giving me TIMEOUT errors for a while now, while the build progresses normally in the Linux and Windows machines T

Re: [Bioc-devel] Build warnings for missing documentation on defunct functions

Hi Roel, A deprecated function is still exported and documented. Inside the function you'll call .Deprecated() and the man page should state it's deprecated and suggest an alternative if appropriate. The process of deprecate, defunct, remove is documented here: https://bioconductor.org/develope

[Bioc-devel] "extra" unit tests

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]] ___

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

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*()` function

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

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 other

Re: [Bioc-devel] Install directly from the bioconductor git repo?

Thank you Martin. Are the core packages being kept as Github mirrors? On Wed, Oct 25, 2017 at 3:21 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 10/24/2017 04:16 PM, Stian Lågstad wrote: > >> Can I install a package directly from a Bioconductor git repository? Like >> I >> can fo