Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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",

Re: [Rd] establishing a Code of Conduct for R

On 13 September 2017 at 13:22, Brian G. Peterson wrote: > I am not an official representative of the R team, so this is only my > opinion. > Thank you. > It seems to me that you are trying to create a solution to a problem > which does not exist. I am not trying to create

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Rd] vcov and survival

Dear Terry, Even the behaviour of lm() and glm() isn't entirely consistent. In both cases, singularity results in NA coefficients by default, and these are reported in the model summary and coefficient vector, but not in the coefficient covariance matrix: > mod.lm <-

[Rd] vcov and survival

I have just noticed a difference in behavior between coxph and lm/glm: if one or more of the coefficients from the fit in NA, then lm and glm omit that row/column from the variance matrix; while coxph retains it but sets the values to zero. Is this something that should be "fixed", i.e.,

[R-pkg-devel] Migrating a package name

Hello, I have a package 'lsmeans' (for "least-squares means") for follow-up analyses of models; and it has become increasingly clear to me that its name is archaic and misleading. It works for GLMs, ordinal and count regression, Bayesian models fitted using MCMC, and all sorts of other models

[Rd] y label for X11 graphics

In the following plot, the y label is missing if it is too long. x11(type="Xlib") plot(1:5, 1:5, ylab="Do, a deer, a female deer") # missing label plot(1:5, 1:5, ylab="Do") # label is present All is well for x11(type="cairo") This is true both under R devel

Re: [Bioc-devel] MultiAssayExperiment Subsetting Fails if Column Data Has One Column

Dear Dario, Thank you for your report, this is resolved in MultiAssayExperiment 1.3.35. Sorry for the noise everyone. Regards, Marcel On 09/12/2017 11:00 PM, Dario Strbenac wrote: > Good day, > > Subsetting a MultiAssayExperiment object fails if the column data has one > column but not 2

Re: [Bioc-devel] ExperimentList Contructor Failing

Hi Dario, You're using a different version of MultiAssayExperiment which might make the original problem less reproducible. I was not able to reproduce the error on the release version of MultiAssayExperiment. If you do find the issue again. Please let me know. As a side note, we are using the

Re: [Bioc-devel] BiocStyle2: issue with wide figure command

Yes, I was indeed sitting on an old Tex version. Upgrading to Tex Live 2017 fixed that. Thanks, Ludwig > Hi Ludwig, > > thank you! This sounds like an issue with your LaTeX distribution, in > particular the package 'marginfix'. Please make sure that all the packages > listed in the BiocStyle

Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

Hi, Simply, for LCMSMS protein identification, it is better to use curated, and verified protein sequence database (from experiments, assays and publications). Uniprot KnowledgeBase is known to be the most curated one (even manually) It will be possible to convert ans improve uniprotKB (Hs) to

Re: [Rd] establishing a Code of Conduct for R

On Wed, 2017-09-13 at 12:54 +0200, Suzen, Mehmet wrote: > Dear Colleagues/Developers/R enthusiasts, > > Would it be possible to develop a code of conduct (CoC) document for > R lists, CRAN submissions that all developers/maintainers to follow? > This may help all of us to better communicate and

Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

Hey guys, Thanks for your responses! Exactly the kind of feedback I wanted, to ensure that what is being intended makes sense. Resource to be used is UniprotKB. Preview the first 10 entries:

Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

Hi, I general LCMSMS generate mass/charge data of Amino Acid or peptides. The goal in to identify which protein belong the peptides. The Software used with LCMSMS can match the peptides to Uniprot database , and ranks putative proteins by scores. Could the tell us what is the interest of

Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

can you say a little more about what resource will be tapped and what it will look like? you can already use uniprot identifiers as keys into org.Hs.eg.db On Tue, Sep 12, 2017 at 9:05 AM, Aditya Bhagwat < adb2...@qatar-med.cornell.edu> wrote: > Hey guys, > > I love the org.Hs.eg.db package (and

[Rd] unpackPkgZip: "unable to move temporary installation" due to antivirus

Hi, Me and an office colleague on Microsoft Windows 10 PCs are having difficulty installing any package. This is a recent issue for us, and we suspect our McAfee antivirus has modified by our IT department. Let's take, for example, install.packages("mypackage"), here is the output: package

Re: [Bioc-devel] failing Bioconductor package DeepBlueR

Dear Hervé, You are right. I found the issue in rtracklayer and made a pull request with a fix. https://github.com/lawremi/rtracklayer/pull/1 Thanks for your help. Best, Markus On Tue, 12 Sep 2017 at 18:01 Hervé Pagès wrote: > Hi Markus, > > The class cache issue is

[R-pkg-devel] CRAN incoming checks / winbuilder on demand results for R-devel

Dear package developers, given some very recent changes in R-devel, many packages under R-devel have to be reinstalled. Due to maintainance work on CRAN we probably won't process submissions today. R-devel results from winbuilder will be flaky at least during the next 10 hours. Best, Uwe

[Rd] CRAN incoming checks / winbuilder on demand results for R-devel

Dear package developers, given some very recent changes in R-devel, many packages under R-devel have to be reinstalled. Due to maintainance work on CRAN we probably won't process submissions today. R-devel results from winbuilder will be flaky at least during the next 10 hours. Best, Uwe

Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

Hi Johannes, Thanks for your feedback! I tried ensembl based maps earlier, but I loose many features. In LCMS proteomics the unit of identification and quantification is a uniprot accession, so annotation mappings would benefit from a uniprot-centric database object. Cheers, Aditya