Re: [Bioc-devel] ExpData in SummarizedExperiment

yes I'll bump DESeq2 in release now [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] ExpData in SummarizedExperiment

Just to clarify: do all packages that define classes on top of SummarizedExperiment need to bump their version number in release to fix? ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] ExpData in SummarizedExperiment

Yes, us too. Users are reporting DESeq2 1.48.0 for Bioconductor 3.21 is failing with something similar: ``` Error in validObject(.Object) : invalid class “DESeqDataSet” object: superclass "ExpData" not defined in the environment of the object's class ``` __

Re: [Bioc-devel] support.bioconductor.org very slow

It has been slow for me from North Carolina, US as well. Maybe since the past 1 or 2 weeks. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

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 m

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 p

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 ma

[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 propaga

Re: [Bioc-devel] Updating for 3.11

I went on a dependency diet and went from 114 to 87 in devel now. I would like to trim more, but I think trimming any of the rest would just be pushing burden over for the user to install packages when they run core functions, so not very helpful. But if someone spots one I can trim, I'd be happy

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

I was thinking 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, Michae

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 poi

[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 perhaps

[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 https://bioconductor.org/packages/re

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

are satisfied with user feedback and >> alterations to create a pull request for the website repository >> > >> > >> > https://github.com/Bioconductor/bioconductor.org >> > >> > >> > >> > >> > Lori Shepherd >> > >&g

[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 postin

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 g...@github.com:ComputationalProteomicsUnit/make

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 temporary

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 th

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 https://stat.ethz

[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

[Bioc-devel] Data package timeouts

I got simultaneous timeout notices for 'airway' and 'parathyroidSE' on both release and devel machines (release was fine leading up to the Bioc release). Not sure what's the issue, I haven't changed these packages in a while. I checked these out and these both build fine and in ~30s on my machine

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

; 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 > wrote: >> >> hi, >> >

[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 rnaseqGene

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 https://stat.ethz.ch/mailman/listinfo/bioc-

[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 Executio

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 https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/data_store/

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 https://stat.ethz.ch/mailman/listinfo/

[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

put them in > S3. Once 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 >

[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 initia

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

riment")) > > 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 AM, Michael Love wrote: >

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

DESeqDataSet,numeric-method" > > [12] "estimateDispersions,DESeqDataSet-method" > > [13] "estimateSizeFactors,DESeqDataSet-method" > > [14] "normalizationFactors,DESeqDataSet-method" > > [15] "normalizationFactors<-,DESeqDataSet,matri

[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 au

[Bioc-devel] best practice for storing long error message in R package

hi, I have a long error message I want to print out after failing on some condition, but don't want this long message taking up space in the body of the function. I'm curious what other developers think would be best practice for where/how to store this message content in a package. best, Mike _

[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 to

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 delet

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") work

Re: [Bioc-devel] TIMEOUTs on Morelia

704) >> ==23105==by 0xD0B6F5A: find_runs_of_ranges (Rle_class.c:837) >> ==23105==by 0xD0B75CA: _subset_Rle_by_ranges (Rle_class.c:996) >> ==23105==by 0xD0B7A42: Rle_extract_ranges (Rle_class.c:1018) >> ==23105==by 0x4F24411: R_doDotCall (dotcode.c:582) >

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 PM, Mic

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 investigate and report back here.

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 < martin.mor...@roswellpark.org>

[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 eve

[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" 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")

[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 wrote: > Hi Michael, Herve, > > > On 6/17/2015 9:43 PM, Hervé Pagès wrote: >> >> Hi Michael, >> >> On 06/17/2015 12:35 AM, Michael Lov

[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 parathyroi

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 wrote: > > >

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 wrote: > > > - Original Message - >> From: "Michael Love" >> To: bioc-devel@r-project.org >> Sent: Wednesday, April 8, 2015 11:03:02 AM >> Subject: [Bioc-devel]

[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

ing a hook to that effect into a user’s R)? >> >> > It's a good idea and one that Eclipse 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. > > Wol

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 t

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

On Fri, Apr 3, 2015 at 7:32 AM, Michael Love 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 th

[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 as

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 wrote: > Hi Michael, > > On 04/01/2015 07:17 AM, Michael Love wrote: >> >> I'll retract th

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

I'll retract those last two emails about empty GRanges. That's simply: se <- SummarizedExperiment(assays, colData=colData) mcols(se) <- myDataFrame On Tue, Mar 31, 2015 at 4:40 PM, Michael Love wrote: > Would this code inspired by the release version of GenomicRanges work?

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

gument of SummarizedExperiment? On Tue, Mar 31, 2015 at 3:49 PM, Michael Love 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. Then

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

w called rowRanges. What's the trick to putting a DataFrame on an empty GRanges, so I can get the old behavior but now using the rowRanges argument? On Tue, Mar 31, 2015 at 3:40 PM, Michael Love wrote: > With GenomicRanges 1.19.48, I'm still having issues with re-naming the > first

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

tools_1.7.0knitr_1.9 [9] 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 wrote: > > > On Mar 9, 2015 12:36 PM, "Martin Morgan" wrote:

Re: [Bioc-devel] testthat instructions for website

On Mar 13, 2015 9:13 PM, "Dan Tenenbaum" wrote: > > > > - Original Message ----- > > From: "Michael Love" > > To: bioc-devel@r-project.org > > Sent: Friday, March 13, 2015 6:06:39 PM > > Subject: [Bioc-devel] testthat instructions f

[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 ht

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

On Mar 9, 2015 12:36 PM, "Martin Morgan" 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 withDi

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

hi all, just a practical issue: I have GenomicRanges version 1.19.42 on my computer which does not have rowRanges defined, although the 1.19.42 version on the Bioc website does have rowRanges in the man page: http://master.bioconductor.org/packages/3.1/bioc/html/GenomicRanges.html So I pass chec

Re: [Bioc-devel] recalling methods

ul here, because the generics and >> classes form an intricate and sometimes ambiguous web, especially when >> multiple inheritance and dispatch are involved. I think we should first >> build better tooling for introspecting S4 and for graph-based modeling and >> analysis o

Re: [Bioc-devel] recalling methods

d for the object. Filtering that down to give methods which are "likely relevant" using the documentation will definitely be a bigger challenge. > > > > On Thu, Dec 4, 2014 at 9:56 AM, Michael Love > wrote: >> >> I was thinking about a request from someone a

[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

Re: [Bioc-devel] plotPCA for BiocGenerics

On Nov 1, 2014 1:29 PM, "Michael Love" wrote: > > As far as the proposal of using the plot() function for all plots, I > think for the biologists who are struggling already to get R going, > and to figure out what kinds of plots are possible, plotMA (and > knowing that

Re: [Bioc-devel] plotPCA for BiocGenerics

ore >>>>> - there are very few interesting data structures that only have one visual >>>>> representation to-rule-them-all... >>>>> >>>>> just my 2c >>>>> >>>>> best >>>>> Thomas >>>

Re: [Bioc-devel] GenomicFiles: chunking

use it > in the other GenomicFiles functions. Maybe it's not confusing but instead > makes the individual steps more clear. What do you think, > > - Should the reader function be separate from the MAP? What are the > advantages? > > - Should READER, MAP, REDUCE be stored in

Re: [Bioc-devel] plotPCA for BiocGenerics

>> object. >> >> In addition, this is the same strategy adopted elsewhere in >> Bioconductor, e.g., for the plotMA method. >> >> Just my two cents. >> >> Best, >> davide >> >> On Mon, Oct 20, 2014 at 11:30 AM, Kevin Coombes < >>

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 p

Re: [Bioc-devel] plotPCA for BiocGenerics

t; objects? In which case, there would already be a perfectly good generic > On Oct 20, 2014 10:27 AM, "Michael Love" > wrote: > >> I noticed that 'plotPCA' functions are defined in EDASeq, DESeq2, DESeq, >> affycoretools, Rcade, facopy, CopyNumber450k, n

[Bioc-devel] plotPCA for BiocGenerics

I noticed that 'plotPCA' functions are defined in EDASeq, DESeq2, DESeq, affycoretools, Rcade, facopy, CopyNumber450k, netresponse, MAIT (maybe more). Sounds like a case for BiocGenerics. best, Mike [[alternative HTML version deleted]] ___ Bi

Re: [Bioc-devel] DESeq2 time series - How to set the experimental design

hi Nadia, The Bioconductor support site for users now lives here: https://support.bioconductor.org I've answered a couple of questions already on how to analyze time series datasets with DESeq2, so maybe take a look around there and feel free to post a question tagged with 'deseq2' if you still h

Re: [Bioc-devel] GenomicFiles: chunking

the weird column name 'init', does this give you what you want? best, Mike On Tue, Sep 30, 2014 at 2:08 PM, Michael Love wrote: > hi Kasper and Valerie, > > In Kasper's original email: > > "I would like to be able to write a MAP function which takes > rang

Re: [Bioc-devel] GenomicFiles: chunking

rom the user-facing function >> internally calling pack()/unpack() to reduce the number of import() >> calls, and then in the end giving back the mean coverage over the >> input ranges. I want this too. >> >> >> https://github.com/Bioconductor/GenomicFileViews/

Re: [Bioc-devel] GenomicFiles: chunking

r to support processing multiple ranges in one operation. > > I am happy to help apart from complaining. > > Best, > Kasper > > On Mon, Sep 29, 2014 at 8:55 AM, Michael Love > wrote: >> >> Thanks for checking it out and benchmarking. We should be more clear >> in t

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 for

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Bioc-devel] Submitting a workflow

y > wrote: >> here's 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 Lo

[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] DESeqDataSetFromMatrix Changes Column Names

hi Dario, Here's some example behavior of SummarizedExperiment (here in devel). The renaming behavior is coming from GenomicRanges. Anyway I can't avoid the duplication of memory in the case of a conflict of colnames of the matrix and the rownames of colData, unless I internally overwrite the row

Re: [Bioc-devel] DESeqDataSetFromMatrix Changes Column Names

Hi Dario, Which version are you using? I think the column names of the matrices in the assays of SummarizedExperiment are coming from the rownames of colData. My priority is to avoid doubling the memory footprint in object creation. I think preserving the colnames of the matrix was relevant to m

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 mor

Re: [Bioc-devel] R: Re: Re: Deseq2 and differentia expression

hi Jarod, Please take a look at the beginner vignette for DESeq2. We explain a lot of the questions you are asking, including how to subset the object based on adjusted p-value. Please take a look a my previous email as well, I demonstrated how to subset the results object. As you can see in the v

Re: [Bioc-devel] MicroRNA analisys

yes you can. Note this is more of a main Bioc mailing list question. On Fri, Jul 11, 2014 at 3:56 AM, jarod...@libero.it wrote: > Dear All!! > Can I use Deseq2 for microRNAseq data? > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/

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 wrote: > Dear Dr, > Thanks so much for clarification!!! > So I try the test of log fold change but I'm bit confusion on the results: > If I

Re: [Bioc-devel] Deseq2 and differentia expression

hi Jarod, On Thu, Jul 10, 2014 at 7:59 AM, jarod...@libero.it wrote: > Hi there!!! > > I have did this code: > SampleTable > <-data.frame(SampleName=metadata$ID_CLINICO,fileName=metadata$NOME, > condition=metadata$CONDITION,prim=metadata$CDT) > ddHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable=S

[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 <- > ah$ensembl.release

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