Re: [Bioc-devel] Package problems due to results() function from other package?

Fine with me to make results() into a generic. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] BiocViews for long read technology

hi, On the new #longread slack channel, we have been discussing how it would be helpful to have a BiocViews dedicated to software for data from long read technology, and LongRead was suggested. Perhaps under Software > Technology > Sequencing? Best, Mike

[Bioc-devel] ExperimentHub: bad restore file magic number (file may be corrupted)

In the latest release, one of my files in ExperimentHub is giving the following error on Bioc machines. I haven't touched these files since they were submitted many years ago to EHub. http://bioconductor.org/checkResults/release/data-experiment-LATEST/alpineData/nebbiolo2-buildsrc.html ... ---

Re: [Bioc-devel] Mac ARM64 binaries available

Thanks everyone! This is a huge help. Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] pre-receive hook declined

partment of Data Science, > Bioconductor Core Team Member > Dana Farber Cancer Institute > > > On Jul 1, 2021, at 1:49 AM, Michael Love > > wrote: > > > > I'm getting a similar error, trying to push commits for a new package > > submission. So this is my fir

Re: [Bioc-devel] pre-receive hook declined

I'm getting a similar error, trying to push commits for a new package submission. So this is my first attempt to push to Bioc git servers for this package. After following instructions from https://bioconductor.org/developers/how-to/git/new-package-workflow/ ... spatialDmelxsim git:(main) > git

Re: [Bioc-devel] proposal for additional seqlevelsStyle

This looks great Hervé! I will work on incorporating this into tximeta when RefSeq transcriptomes are used. I second Robert's position that seqlevelsStyle() is one of the most influential contributions to human genetics. ___ Bioc-devel@r-project.org

[Bioc-devel] DESeq2 use of assays<-, fixed in v1.27.26

hi, Just a short note to developers who have a dependency on DESeq2. The development version of DESeq2 was giving error the past day because of a new change to assays<- regarding dimnames, I've just now fixed this use of assays() throughout, so DESeq2 1.27.26 should build without error and

Re: [Bioc-devel] Updating for 3.11

Thanks for the note Karl, and sorry for the break. For others, the change in DESeq2::lfcShrink is that now type="apeglm" is the default instead of type="normal". For the past two releases, users have been getting a message when they run with the default argument that type="normal" performs worse

Re: [Bioc-devel] Block bootstrap for GenomicRanges

Maybe we can break off to a #blockboot channel on the Bioc-community Slack. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Block bootstrap for GenomicRanges

king about will break if two features in y share the same start position, so that's not good. On Mon, Aug 13, 2018 at 11:58 PM, Hervé Pagès wrote: > That helps. I think I start to understand what you are after. > > See below... > > > On 08/13/2018 06:07 PM, Michael Love wrote: &g

Re: [Bioc-devel] Block bootstrap for GenomicRanges

dear Hervé, Thanks for the quick reply about directions to take this. I'm sorry for not providing sufficient detail about the goal of block bootstrapping in my initial post. Let me try again. For a moment, let me ignore multiple chromosomes/seqs and just focus on a single set of IRanges. The

[Bioc-devel] Block bootstrap for GenomicRanges

dear Bioc-devels, >From a conversation on Twitter [1], I've been wondering if there has been any work to implement block bootstrap for GRanges. I guess that's my main question, and then the rest is details and ideas in case it hasn't already been done. The block bootstrap helps to create

[Bioc-devel] workflows are missing from landing pages

It seems like the vignettes are not showing up here: https://bioconductor.org/packages/release/workflows/ https://bioconductor.org/packages/release/workflows/html/rnaseqGene.html https://bioconductor.org/packages/release/workflows/html/RnaSeqGeneEdgeRQL.html

Re: [Bioc-devel] Suggested edits to support site posting guide

t; Lori Shepherd >> > >> > Bioconductor Core Team >> > >> > Roswell Park Cancer Institute >> > >> > Department of Biostatistics & Bioinformatics >> > >> > Elm & Carlton Streets >> > >> > Buffalo, New York

[Bioc-devel] Suggested edits to support site posting guide

dear all, I've edited the text from the posting guide to update it a bit. For example, some of the text still referred to the mailing list ​: ​ "Compose a new message with a new subject line". ​Mostly, though, I wanted to emphasize

Re: [Bioc-devel] Thanks to Andrzej...

Thanks Andrzej! these have been really useful contributions to the Bioc ecosystem [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Nightly builds

I've found this Makefile from Laurent et al makes it a lot easier to do build/check, getting closer to the ease of devtools while still building and checking from command line: https://github.com/ComputationalProteomicsUnit/maker You do: git clone

Re: [Bioc-devel] workflow page reorganization

This already looks much improved, thanks Andrzej and Aaron. I think workflows are where it's at, and this page is probably underappreciated by Bioconductor users and the outside community. My wishlist for the workflows page, which may exceed what is available for the current effort: 1) It should

Re: [Bioc-devel] BiocFileCache for developers

thanks Henrik, I like the explicitness of the `R.cache` approach and I copied it for my current implementation. For the BiocFileCache location that should be used for this package I'm developing, `tximeta`, I'm now using the following logic: * If run non-interactively, `tximeta` uses a

Re: [Bioc-devel] BiocFileCache for developers

user_cache_dir(appname="mikes-package-name") wow, how did you guess it? I'm storing TxDb's for use across sessions with `rname` set to the basename of the GTF file, e.g. "gencode.v27.annotation.gtf.gz". I want to encourage the serendipitous case that there is already a BiocFileCache entry with

Re: [Bioc-devel] BiocFileCache for developers

One solution if a developer really wants to make sure the user knows that the function will store a cache somewhere would be to leave the BiocFileCache location argument without a default value. ___ Bioc-devel@r-project.org mailing list

[Bioc-devel] BiocFileCache for developers

hi, I'm writing a function which currently uses BiocFileCache to store a small data.frame and one or more TxDb objects, so that these objects are persistent and available across sessions (or possible available to multiple users). In the simplest case, I would call bfc <- BiocFileCache() inside

Re: [Bioc-devel] workflow builder error: winbuilder1 says "pdflatex is not available"

ually reinstalling or > reconfiguring anything on the builder. Maybe this was a transient issue > related to the fact that I updated the LaTeX distro on the builder some days > ago. > > Best, > Andrzej > > > On Thu, Sep 14, 2017 at 6:08 PM, Michael Love <michaelisaiahl

[Bioc-devel] workflow builder error: winbuilder1 says "pdflatex is not available"

hi, I pushed a change to rnaseqGene workflow and only winbuilder1 had a problem: * checking PDF version of manual ...Warning: running command '"C:/Progra~1/R/R-3.4.0/bin/x64/Rcmd.exe" Rd2pdf --batch --no-preview --build-dir="C:/Windows/TEMP/RtmpE9T1fB/Rd2pdff6059a733c8" --no-clean -o

Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta

alpine, which had this error as of Sunday, is now cleared (I didn't make any changes to the code) http://master.bioconductor.org/checkResults/devel/bioc-LATEST/alpine/ ___ Bioc-devel@r-project.org mailing list

[Bioc-devel] tximport fails to build on Windows

Anyone have any ideas for how to debug this? I get an error from the tximport vignette on tokay2, but I can't figure out what could be the issue: ... 1 Quitting from lines 185-189 (tximport.Rmd) Error: processing vignette 'tximport.Rmd' failed with diagnostics: cannot open the connection

Re: [Bioc-devel] "access forbidden" trying to add new data to experiment package

That worked. Thanks Martin ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] "access forbidden" trying to add new data to experiment package

hi, After checking out the data_store version, I get an svn error "access forbidden". Can you remind me the proper steps (I tried to following variations on the Source Code instructions for experiment packages)? love:test/ $ svn co

Re: [Bioc-devel] "single cell" BiocViews

That looks right to me, as it spans across transcription, etc. There are so many great single cell methods now on Bioconductor. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list

[Bioc-devel] "single cell" BiocViews

It would be useful to have a "single cell" BiocViews -Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Experimental data package or ExperimentHub

that's done we'll test the package functions and put the > package through a review on the new tracker. > > Val > > > > On 06/30/2016 09:27 AM, Michael Love wrote: > > I want to generate an experimental data package with a small subset of > > alignments. The end goal

[Bioc-devel] Experimental data package or ExperimentHub

I want to generate an experimental data package with a small subset of alignments. The end goal is a software vignette, where the user would specify BAM files. I'd like to try out the ExperimentHub submission process, which is for R data objects. Does it sound reasonable if I were to have an

Re: [Bioc-devel] Listing package-specific methods

(class="RangedSummarizedExperiment")) > > Maybe this could be handled by methods() itself e.g. with > an extra argument that lets the user choose if s/he wants to see > all the methods (i.e. specific + inherited) or only the specific > ones? > > H. > > On 06/27/2016 09:39

Re: [Bioc-devel] Listing package-specific methods

ot;dispersions<-,DESeqDataSet,numeric-method" > > [12] "estimateDispersions,DESeqDataSet-method" > > [13] "estimateSizeFactors,DESeqDataSet-method" > > [14] "normalizationFactors,DESeqDataSet-method" > > [15] "normalizationFact

[Bioc-devel] Listing package-specific methods

hi, Following on a conversation from Bioc2016, I think it would be good to have a function available to Bioconductor users that helps in the following situation: I'm a user, trying out a new package 'foo', which defines the FooData class, that builds on top of SummarizedExperiment. The package

[Bioc-devel] workflow builder "Failed to check repository revision..."

hi, I committed a new version of the rnaseqGene workflow about an hour ago and am waiting on the workflow builder to start running. There may be something going on here: Started on Mar 1, 2016 10:28:00 AM Received SCM poll call on master for rnaseqGene on Mar 1, 2016 10:28:01 AM ERROR: Failed

Re: [Bioc-devel] workflows running Bioc-devel

+1 I'm also interested in having the option of devel / release workflow branches for the reasons Aaron mentions. I develop software and workflow in tandem but currently there is a disconnect in showing publicly how software changes will impact a workflow. [[alternative HTML version

Re: [Bioc-devel] package citation and version is not updated

hi Dan, I'm having the same issue with tximport: http://bioconductor.org/packages/devel/bioc/html/tximport.html The CITATION file has been in there since the package was added to devel last week https://github.com/Bioconductor-mirror/tximport/blob/master/inst/CITATION citation("tximport")

Re: [Bioc-devel] TIMEOUTs on Morelia

​Thanks Stephen and Dan, sorry I haven't chased this down recently. I have access to a Mac and will look into it now. -Mike​ On Mon, Feb 1, 2016 at 1:45 PM, Dan Tenenbaum wrote: > Actually, it does seem like there is a more complicated issue going on. I > will

Re: [Bioc-devel] TIMEOUTs on Morelia

I was able to construct a minimal example where it seems the bug originates from SummarizedExperiment: library(SummarizedExperiment) se <- SummarizedExperiment(matrix(1:6,ncol=2)) rse <- as(se, "RangedSummarizedExperiment") rse[1:2,] # hangs On Mon, Feb 1, 2016 at 2:57

Re: [Bioc-devel] TIMEOUTs on Morelia

2) >> ==23105==by 0x4F31621: do_dotcall (dotcode.c:1251) >> ==23105==by 0x4F6FA8A: Rf_eval (eval.c:713) >> ==23105==by 0x4F88101: do_begin (eval.c:1806) >> ==23105==by 0x4F6F8B7: Rf_eval (eval.c:685) >> ==23105==by 0x4F85303: Rf_applyClosure (eval.c:1134) &g

Re: [Bioc-devel] ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position?

thanks for the heads up Lorena and Martin I've just checked in a DESeq2 using importFrom of ggplot2 functions I now just have one warning for DESeq2 CHECK: Warning: multiple methods tables found for ‘relistToClass’ On Sat, Dec 19, 2015 at 2:02 PM, Morgan, Martin <

[Bioc-devel] Bioc twitter bot is on repeat

best said by James Eddy: "Could someone please put out a new @Bioconductor package so @Bioconductor stops tweeting about the same 3 every day?" https://twitter.com/jamesaeddy/status/668911442007949313 https://twitter.com/Bioconductor [[alternative HTML version deleted]]

Re: [Bioc-devel] as.character method for GenomicRanges?

+1 I was in need of this function yesterday and generally about once a week, when looking up ranges in IGV or UCSC. On Tue, Sep 15, 2015 at 12:59 PM, Michael Lawrence < lawrence.mich...@gene.com> wrote: > Did this as.character method ever get added? It was a good idea, and we > should add it

[Bioc-devel] Bioc workflows: using rmarkdown as vignette engine

hi Dan, (I add bioc-devel as this might be useful info for others) Is it possible to specify rmarkdown as the vignette engine for workflows? The citation functionality [1] of rmarkdown would be useful, as there is discussion to have workflows possible submitted as peer reviewed papers. I tried

Re: [Bioc-devel] testing class and length of function args

Thanks all for the pointers On Jul 23, 2015 10:51 AM, Charles C. Berry ccbe...@ucsd.edu wrote: On Wed, 22 Jul 2015, Michael Love wrote: it's slightly annoying to write foo - function(x) { if ( ! is.numeric(x) ) stop(x should be numeric) if ( ! length(x) == 2 ) stop(x should be length 2

[Bioc-devel] testing class and length of function args

it's slightly annoying to write foo - function(x) { if ( ! is.numeric(x) ) stop(x should be numeric) if ( ! length(x) == 2 ) stop(x should be length 2) c(x[2], x[1]) } i wonder if we could have some core functions that test the class and the length in one and give the appropriate stop

Re: [Bioc-devel] making txdb, and propagating metadata from AnnotationHub to GenomicFeatures

that's great Hervé and Sonali! thanks for the quick response. best, m On Thu, Jun 18, 2015 at 10:07 AM, Sonali Arora sar...@fredhutch.org wrote: Hi Michael, Herve, On 6/17/2015 9:43 PM, Hervé Pagès wrote: Hi Michael, On 06/17/2015 12:35 AM, Michael Love wrote: Background

[Bioc-devel] making txdb, and propagating metadata from AnnotationHub to GenomicFeatures

Background: With previous approaches that I would recommend to users for building txdb along the way of making count tables, it was desirable that the GTF release information would *automatically* be passed into the metadata of the rowRanges of the SummarizedExperiment. for example, in

Re: [Bioc-devel] RSS package feeds not updated

I have another small request, when the RSS feed returns to normal it says No build problems for myPackage. Could this title indicate whether it is referring to release or devel? I'm totally happy with the feed behavior otherwise. On Wed, Dec 3, 2014 at 3:07 PM, Dan Tenenbaum

Re: [Bioc-devel] request for more notices about build issues

works for me. Thanks Dan. On Tue, Apr 14, 2015 at 2:34 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Michael Love michaelisaiahl...@gmail.com To: bioc-devel@r-project.org Sent: Wednesday, April 8, 2015 11:03:02 AM Subject: [Bioc-devel] request for more

[Bioc-devel] request for more notices about build issues

dear core Bioc-ers, It would be nice to have more devel mailing list notices about large scale build issues, just to keep developers in the loop. (e.g. I often get a number of emails when GenomicRanges is down, asking why I'm breaking someone's downstream package). Or if you don't want to push

Re: [Bioc-devel] recalling methods

and other IDEs use for auto-completion. We'd just have to find the right codebase, i.e., something with a lot of end-user analysis code, instead of infrastructure. Wolfgang On Dec 6, 2014, at 1:19 GMT+1, Michael Love michaelisaiahl...@gmail.com wrote: nice. I will play around

[Bioc-devel] SummarizedExperiment, differing assay dimnames

hi Martin, I noticed with GenomicRanges 1.19.51, a new, or newly functional, check on dimnames differing between assays. It might be convenient to add an option that assays() will take an incoming matrix without error no matter what, even if the dimnames on the incoming matrix are not the same

Re: [Bioc-devel] SummarizedExperiment, differing assay dimnames

On Fri, Apr 3, 2015 at 7:32 AM, Michael Love michaelisaiahl...@gmail.com wrote: hi Martin, I noticed with GenomicRanges 1.19.51, a new, or newly functional, check on dimnames differing between assays. ah, I'm still using 1.19.50, maybe that's the issue. But I'd still like to hear what the new

Re: [Bioc-devel] Build error for DESeq2 dev causing error in other package builds

hi Andrea, I sent out an email to bioc-devel at the same time as you :) https://stat.ethz.ch/pipermail/bioc-devel/2015-April/007269.html I think this might be fixed already, but I didn't have time to try out GenomicRanges 1.19.51 yet. I will try soon, and if this doesn't fix it, I have a hack

Re: [Bioc-devel] Changes to the SummarizedExperiment Class

Yes, you're right! Sorry for the noise. I forgot this was how it always behaved. All I had to do was change the argument name. On Wed, Apr 1, 2015 at 3:51 PM, Hervé Pagès hpa...@fredhutch.org wrote: Hi Michael, On 04/01/2015 07:17 AM, Michael Love wrote: I'll retract those last two emails

Re: [Bioc-devel] Changes to the SummarizedExperiment Class

] BiocInstaller_1.17.6 loaded via a namespace (and not attached): [1] formatR_1.1XVector_0.7.4 tools_3.3.0stringr_0.6.2 evaluate_0.5.5 On Mon, Mar 9, 2015 at 1:21 PM, Michael Love michaelisaiahl...@gmail.com wrote: On Mar 9, 2015 12:36 PM, Martin Morgan mtmor...@fredhutch.org wrote: On 03/09/2015

Re: [Bioc-devel] Changes to the SummarizedExperiment Class

of SummarizedExperiment? On Tue, Mar 31, 2015 at 3:49 PM, Michael Love michaelisaiahl...@gmail.com wrote: I forgot to ask my other question. I had gone in early March and fixed my code to eliminate rowData-, but the argument to SummarizedExperiment was still called rowData, and a DataFrame could be provided

[Bioc-devel] testthat instructions for website

hi Bioc team, Can we add some testthat instructions to the unit testing page: http://bioconductor.org/developers/how-to/unitTesting-guidelines/ I presume the instructions would be simply to follow the basic testthat instructions, e.g.: https://github.com/hadley/testthat/blob/master/README.md

Re: [Bioc-devel] Changes to the SummarizedExperiment Class

Some guidance on how to avoid duplication of the matrix for developers would be greatly appreciated. Another example of a trouble point, is that if I am given an SE with an unnamed assay and I need to give the assay a name, this also can expand the memory used. I had found a solution (which works

Re: [Bioc-devel] Changes to the SummarizedExperiment Class

On Mar 9, 2015 12:36 PM, Martin Morgan mtmor...@fredhutch.org wrote: On 03/09/2015 08:07 AM, Michael Love wrote: Some guidance on how to avoid duplication of the matrix for developers would be greatly appreciated. It's unsatisfactory, but using withDimnames=FALSE avoids duplication

Re: [Bioc-devel] recalling methods

or more end-user UIs? On Fri, Dec 5, 2014 at 11:05 AM, Michael Love michaelisaiahl...@gmail.com wrote: On Thu, Dec 4, 2014 at 4:01 PM, Michael Lawrence lawrence.mich...@gene.com wrote: I think this gets at the heart of at least one of the usability issues in Bioconductor: interface

[Bioc-devel] recalling methods

I was thinking about a request from someone at Bioc2014 (I can't remember at the moment) As an end-user, if I have an object x, how can I *quickly* recall the main methods for that? As in, without breaking my flow and going to ?myClass or help(myClass-class). Suppose x is a GRanges, how can I

Re: [Bioc-devel] plotPCA for BiocGenerics

version of the plot generic for this class. And you could tweak the as.PCA function so it returns an object of the mySpecialPCA class. And the user could still just plot the result without hacving to care what's happening behind the scenes. On 10/20/2014 5:59 PM, Michael Love wrote: Ah, I see now

Re: [Bioc-devel] GenomicFiles: chunking

' for lack of a better term. We could also go with 'reducedData' or another suggestion. Thanks for the feedback. Valerie On 10/01/2014 08:30 AM, Michael Love wrote: hi Kasper, For a concrete example, I posted a R and Rout file here: https://gist.github.com/mikelove/deaff84dc75f125d

Re: [Bioc-devel] plotPCA for BiocGenerics

objects? In which case, there would already be a perfectly good generic On Oct 20, 2014 10:27 AM, Michael Love michaelisaiahl...@gmail.com wrote: I noticed that 'plotPCA' functions are defined in EDASeq, DESeq2, DESeq, affycoretools, Rcade, facopy, CopyNumber450k, netresponse, MAIT (maybe

Re: [Bioc-devel] plotPCA for BiocGenerics

I agree it depends on programming style. But to continue with the example, it would have to be: plot(as.mySpecialObjectPCA(mySpecialObject)) because we have many packages here with their own functions. Wouldn't this just proliferate the number of classes instead of functions? For every type of

Re: [Bioc-devel] plotPCA for BiocGenerics

plotPCA as follows: plotPCA - function(object, ...) { plot(as.PCA(object), ...) } This would be relatively easy to eventually deprecate and teach users to switch to the alternative. On 10/20/2014 1:07 PM, Michael Love wrote: hi Kevin, that would imply there is only one way to plot

Re: [Bioc-devel] GenomicFiles: chunking

column name 'init', does this give you what you want? best, Mike On Tue, Sep 30, 2014 at 2:08 PM, Michael Love michaelisaiahl...@gmail.com wrote: hi Kasper and Valerie, In Kasper's original email: I would like to be able to write a MAP function which takes ranges, file instead of just

Re: [Bioc-devel] GenomicFiles: chunking

Thanks for checking it out and benchmarking. We should be more clear in the docs that the use case for reducing by range is when the entire dataset won't fit into memory. Also, we had some discussion and Valerie had written up methods for packing up the ranges supplied by the user into a better

Re: [Bioc-devel] GenomicFiles: chunking

complaining. Best, Kasper On Mon, Sep 29, 2014 at 8:55 AM, Michael Love michaelisaiahl...@gmail.com wrote: Thanks for checking it out and benchmarking. We should be more clear in the docs that the use case for reducing by range is when the entire dataset won't fit into memory. Also, we had

[Bioc-devel] Submitting a workflow

hi, I'd like to contribute a workflow, but I don't see a guide on how to submit a workflow on the website. Do the workflows have the same versioning system x.y.z as software packages? Is it possible to use the github bridge with workflows? thanks, Mike

Re: [Bioc-devel] Submitting a workflow

the guide i am aware of. a link should be on the basic workflow page as a 'how to'. https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/README.md On Wed, Sep 3, 2014 at 7:47 AM, Michael Love michaelisaiahl...@gmail.com wrote: hi, I'd like to contribute a workflow, but I don't see

Re: [Bioc-devel] [BioC] More than one package document with the same name

(copying over to bioc-devel). I do appreciate the very few keystrokes it takes to do, e.g. vignette('affy') of course I can find them all with browseVignettes('affy') and sometimes the above is not the right name, but I like that the primary documentation is so close at hand. this is slightly

Re: [Bioc-devel] Deseq2 and differentia expression

hi Jarod, This is more of a main Bioc mailing list question, so you can address future questions there. On Fri, Jul 11, 2014 at 6:05 AM, jarod...@libero.it jarod...@libero.it wrote: Dear Dr, Thanks so much for clarification!!! So I try the test of log fold change but I'm bit confusion on the

[Bioc-devel] makeTranscriptDbFrom... AnnotationHub

The recent TranscriptDb thread reminded me of a question: are there plans (or am I missing the function) to easily get a TranscriptDb out of the AnnotationHub objects? It would be great to have a preprocessed Ensembl txdb like we have for UCSC. ah - AnnotationHub() gr -

Re: [Bioc-devel] Problem on Installation of DEseq2

hi Jarod, What version of Rcpp and RcppArmadillo is installed? Mike On Wed, Jun 18, 2014 at 11:35 AM, jarod...@libero.it jarod...@libero.it wrote: I can't install this DESEq2 on the RHEL 5.5 server: * installing *source* package ‘RcppArmadillo’ ... ** package

Re: [Bioc-devel] Problem on Installation of DEseq2

are you installing with: biocLite(DESeq2) hmm these don't look like Rcpp* version numbers. What do you get with library(Rcpp) library(RcppArmadillo) sessionInfo() On Wed, Jun 18, 2014 at 1:13 PM, jarod...@libero.it jarod...@libero.it wrote: Thanks for your help I have the 2.0 when i try to

[Bioc-devel] change names(assays(SummarizedExperiment)) w/o copy?

hi, Is there a way that I can change the names of the assays slot of a SummarizedExperiment, without making a new copy of the data contained within? Assume I get an SE which has already been constructed, but no names on the assays() SimpleList. thanks, Mike library(GenomicRanges) gc()

Re: [Bioc-devel] 'droplevels' argument in `[` method for SummarizedExperiment?

At the least, I will add the use of droplevels on colData to the vignette. On Mar 12, 2014 7:28 PM, Steve Lianoglou lianoglou.st...@gene.com wrote: On Wed, Mar 12, 2014 at 3:52 PM, Michael Lawrence lawrence.mich...@gene.com wrote: On Wed, Mar 12, 2014 at 3:45 PM, Martin Morgan

[Bioc-devel] BigWigViews

a discussion came up on devel last year about looking at a genomic range over multiple samples and multiple experiments ( https://stat.ethz.ch/pipermail/bioc-devel/attachments/20120920/93a4fb61/attachment.pl ) stepping aside the multiple experiment part, I'm interested in BigWigViews() with

Re: [Bioc-devel] BigWigViews

kasperdanielhan...@gmail.com wrote: (Michael Love and I had some discussion on this Friday) I also think it would be a very convenient class/method. A lot of data these days are naturally represented (and are available from say GEO) as bigWig files (essentially coverage tracks

Re: [Bioc-devel] renameModelMatrixColumns mishap + patch for DESeq2

hi Steve, I have fixed this bug in version 1.0.18 and 1.1.22, and I added a unit test for such a design formula in the devel version. best, Mike On Wed, Jul 10, 2013 at 8:52 AM, Michael Love michaelisaiahl...@gmail.com wrote: Hi Steve, Thanks for pointing out this bug in the renaming code

Re: [Bioc-devel] DESeq2 and miscTranformsation(s)

)$dispersion - NULL then either rlogTransformation or varianceStabilizingTransformation, which will call estimateDispersions internally. Mike On Sun, Apr 21, 2013 at 8:13 PM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: Hi Michael, On Sat, Apr 20, 2013 at 12:18 AM, Michael Love