[BioC] ggbio 1.12.0 autoplot() with txdb example is broken

[Dan Tenenbaum]

----- Original Message -----
> From: "Leonardo Collado Torres" <lcollado at jhu.edu>
> To: "Tengfei Yin" <tengfei.yin at sbgenomics.com>
> Cc: "Dan Tenenbaum" <dtenenba at fhcrc.org>, "Bioconductor mailing list" <bioconductor at r-project.org>
> Sent: Wednesday, April 23, 2014 3:32:20 PM
> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken
> 
> Hi Dan,
> 
> I got RSwitch to work with a second installation of R 3.1. Basically,
> I downloaded the leopard tarball, expanded it, renamed the folder 3.1
> to 3.1patched (which is the version I downloaded, but well, anything
> except for 3.1 would work), compressed it again, and then expanded it
> at the root location.
> 
> So it would be something like this:
> 
> wget
> http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch-snowleopard-sa-x86_64.tar.gz
> tar -xvf R-*gz
> mv Library/Frameworks/R.framework/Versions/3.1
> Library/Frameworks/R.framework/Versions/3.1patched
> tar -cvzf Rlib.tgz Library
> sudo tar fvxz Rlib.tgz -C /
> 
> Then used RSwitch, and was able to install BioC-devel.
> 

That's good to know. I usually install from the installer (.pkg file) not the tarball, so I didn't think of this approach.

Dan


> I might try out your `renv` at a different time. It's great to know
> that it exists =)
> 
> Cheers,
> Leo
> 
> 
> On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin
> <tengfei.yin at sbgenomics.com> wrote:
> > Hi Dan,
> >
> > It works like a charm, thanks!
> >
> > I use your method, then I changed /Library/Framework/ folder and
> > R.Framework
> > folder ownership to myself so I don't have to sudo it, then I just
> > add alias
> > to "emacs2" and "emacs3" to run your renv to switch the R first.
> > This solves
> > my problem.
> >
> > Try to customize variable for R hooks in emacs as alternative
> > solution, but
> > may need more time.
> >
> > Thanks again!
> >
> > Tengfei
> >
> >
> > On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
> > wrote:
> >>
> >> Hi Tengfei,
> >>
> >> ----- Original Message -----
> >> > From: "Tengfei Yin" <tengfei.yin at sbgenomics.com>
> >> > To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> >> > Cc: "Bioconductor mailing list" <bioconductor at r-project.org>,
> >> > lcollado at jhu.edu
> >> > Sent: Wednesday, April 23, 2014 11:01:18 AM
> >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is
> >> > broken
> >> >
> >> >
> >> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on the R
> >> > 3.1?
> >>
> >> Yes, install two copies of R 3.1 and switch between them.
> >>
> >> > And do some sort of switch for bioc? The website you send to me
> >> > also
> >> > have a R-devel build, my plan is to install bioc 3.0 on R-devel
> >> > and
> >> > bioc 2.14 on R 3.1, and do some tricks with emacs for R only to
> >> > switch bioc, so that I could debug and maintain released and
> >> > devel
> >> > version.
> >>
> >> PLEASE don't use R-devel at all.
> >>
> >> Just use R-3.1.0.
> >>
> >> You can use the Rswitch app but as you point out it won't work
> >> within
> >> emacs.
> >>
> >> This is what I do:
> >>
> >> Every time I download a new version of R, I run its installer. The
> >> installer always puts it in
> >>
> >> /Library/Frameworks/R.framework
> >>
> >> So after I install each version of R, I rename the R.framework
> >> directory
> >> to something like
> >> R.framework.bioc214_snowleopard
> >>
> >> And then I make a symlink from R.framework.bioc214_snowleopard to
> >> R.framework.
> >>
> >> I have a little script at https://github.com/dtenenba/renv which
> >> lets me
> >> see what the various installed Rs are:
> >>
> >> $ renv
> >> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0
> >> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0
> >> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0
> >> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0
> >> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0
> >>
> >> This tells me that the currently active R is nicknamed
> >> "releaseMav" (this
> >> means there is a link from
> >> /Library/Frameworks/R.framework.releaseMav to
> >> /Library/Frameworks/R.framework. It shows the versions, svn
> >> revisions,
> >> dates, and architectures of each version. (darwin10.8.0 is Snow
> >> Leopard;
> >> darwin13.1.0 is Mavericks).
> >>
> >> Note that in my nomenclature devel means BioC devel, not R-devel.
> >>
> >> So if I wanted to switch to the "develSL" version I would do:
> >>
> >> sudo renv develSL
> >>
> >> HTH
> >> Dan
> >>
> >>
> >>
> >> >
> >> >
> >> >
> >> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum <
> >> > dtenenba at fhcrc.org >
> >> > wrote:
> >> >
> >> >
> >> >
> >> > Hi Tengfei,
> >> >
> >> > ----- Original Message -----
> >> > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
> >> >
> >> > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org >
> >> > > Cc: "Bioconductor mailing list" < bioconductor at r-project.org
> >> > > >,
> >> > > lcollado at jhu.edu
> >> >
> >> > > Sent: Wednesday, April 23, 2014 10:46:02 AM
> >> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example
> >> > > is
> >> > > broken
> >> > >
> >> > >
> >> >
> >> > > Thanks a lot Dan! it's clear to me now, sorry that I am still
> >> > > a
> >> > > newbie to OSX ... I got R-devel running and I will try
> >> > > Rswitcher, I
> >> > > also want to do that switch easily in emacs too.
> >> > >
> >> > >
> >> >
> >> > You don't want to use R-devel. Both BioC release (2.14) and BioC
> >> > devel (3.0) are meant to work with R-3.1.0, the released version
> >> > of
> >> > R.
> >> >
> >> > I think the Rswitch app just sets a symbolic link, so you should
> >> > be
> >> > able to do that within emacs. Run it and see what it does to
> >> > /Library/Frameworks/R.framework.
> >> >
> >> > Dan
> >> >
> >> >
> >> > >
> >> > > cheers
> >> > >
> >> > >
> >> > > Tengfei
> >> > >
> >> > >
> >> > >
> >> >
> >> >
> >> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum <
> >> > > dtenenba at fhcrc.org
> >> > > >
> >> > > wrote:
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > ----- Original Message -----
> >> > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
> >> > >
> >> > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org >
> >> > > > Cc: "Bioconductor mailing list" < bioconductor at r-project.org
> >> > > > >,
> >> > > > lcollado at jhu.edu
> >> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM
> >> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb
> >> > > > example is
> >> > > > broken
> >> > > >
> >> > > >
> >> > >
> >> > > > Hi Dan,
> >> > > >
> >> > > >
> >> > > > So you mean I install R 3.1 for snow leopard and it should
> >> > > > work?
> >> > >
> >> > > Yes.
> >> > >
> >> > >
> >> > >
> >> > > ? Is
> >> > > > there a way to build from source using biocLite, like type =
> >> > > > "source", this is what I got
> >> > > >
> >> > > >
> >> > > >
> >> > > > > library(BiocInstaller)
> >> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite
> >> > > > for
> >> > > > help
> >> > > > > biocLite("GenomicRanges")
> >> > > > BioC_mirror: http://bioconductor.org
> >> > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R
> >> > > > version
> >> > > > 3.1.0.
> >> > > > Installing package(s) 'GenomicRanges'
> >> > > >
> >> > > >
> >> > > > package ‘GenomicRanges’ is available as a source package but
> >> > > > not
> >> > > > as
> >> > > > a
> >> > > > binary
> >> > > >
> >> > > >
> >> > > > Warning message:
> >> > > > package ‘GenomicRanges’ is not available (for R version
> >> > > > 3.1.0)
> >> > > >
> >> > > >
> >> > > > Just wondering is there a solution without re-install R for
> >> > > > snow
> >> > > > leopard. And what's the plan for maverick?
> >> > > >
> >> > >
> >> > > You can do
> >> > > biocLite("GenomicRanges", type="source")
> >> > >
> >> > > but you need to have the appropriate compilers, etc.
> >> > >
> >> > > I *STRONGLY* recommend using the Snow Leopard build. You can
> >> > > have
> >> > > multiple installations of R on your Mac and switch between
> >> > > them
> >> > > using Rswitch ( http://r.research.att.com/#other ) or another
> >> > > easy
> >> >
> >> >
> >> > > mechanism.
> >> > >
> >> > > We are building packages for Mavericks now, we just have to
> >> > > resolve
> >> > > a
> >> > > few build issues and test the resulting packages, we still
> >> > > hope to
> >> > > have them available by the end of the month. But since you can
> >> > > install the Snow Leopard build without needing to remove your
> >> > > Mavericks build, you should do that.
> >> > >
> >> > > Dan
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > >
> >> > > > Thanks
> >> > > >
> >> > > >
> >> > > > Tengfei
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum <
> >> > > > dtenenba at fhcrc.org
> >> > > > > wrote:
> >> > > >
> >> > > >
> >> > > > Hi Tengfei,
> >> > > >
> >> > > >
> >> > > > ----- Original Message -----
> >> > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
> >> > > > > To: lcollado at jhu.edu
> >> > > > > Cc: bioconductor at r-project.org
> >> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM
> >> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb
> >> > > > > example
> >> > > > > is
> >> > > > > broken
> >> > > > >
> >> > > > > btw, based on the error, let me try to debug it.
> >> > > > >
> >> > > > >
> >> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin
> >> > > > > < tengfei.yin at sbgenomics.com >wrote:
> >> > > > >
> >> > > > > > Hi Leonardo,
> >> > > > > >
> >> > > > > > Frankly speaking, the vignette is still in progress, and
> >> > > > > > there
> >> > > > > > are
> >> > > > > > some
> >> > > > > > known bugs in ggbio I need to fix (still trying to find
> >> > > > > > a
> >> > > > > > time
> >> > > > > > to
> >> > > > > > do that
> >> > > > > > ... ), I am recently trying to install R 3.1 and Bioc
> >> > > > > > 2.14 on
> >> > > > > > my
> >> > > > > > new MBP
> >> > > > > > with OSX 10.9, but fails, probably binary build is not
> >> > > > > > ready
> >> > > > > > for
> >> > > > > > maverick
> >> > > > > > yet, maybe available by the end of April?
> >> > > > > >
> >> > > > > > Thanks for reporting the bug, I will keep you posted on
> >> > > > > > this
> >> > > > > > when
> >> > > > > > I
> >> > > > > > successfully get it on my laptop and start fixing the
> >> > > > > > problems.
> >> > > > > >
> >> > > >
> >> > > > You can install the Snow Leopard build of R and should have
> >> > > > no
> >> > > > problems, binary packages are available for that version. It
> >> > > > will
> >> > > > run fine on Mavericks.
> >> > > >
> >> > > > Dan
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > > > > cheers
> >> > > > > >
> >> > > > > > Tengfei
> >> > > > > >
> >> > > > > >
> >> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado
> >> > > > > > Torres <
> >> > > > > > lcollado at jhsph.edu > wrote:
> >> > > > > >
> >> > > > > >> Hello Tengfei + bioc list,
> >> > > > > >>
> >> > > > > >> From
> >> > > > > >>
> >> > > > > >> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst/doc/ggbio.pdf
> >> > > > > >> page 4 (complied on april 11 2014), the following
> >> > > > > >> example
> >> > > > > >> loads
> >> > > > > >> to
> >> > > > > >> an
> >> > > > > >> error as shown below. I wasn't seeing this error before
> >> > > > > >> (aka,
> >> > > > > >> last
> >> > > > > >> week). The only guess that comes to mind is the recent
> >> > > > > >> update
> >> > > > > >> to
> >> > > > > >> GenomicRanges (1.16.2) although that doesn't seem to be
> >> > > > > >> related
> >> > > > > >> from
> >> > > > > >> the traceback() output, well... maybe it's related to
> >> > > > > >> the
> >> > > > > >> ignore.strand = TRUE part as described in the error.
> >> > > > > >>
> >> > > > > >> I'll create a GitHub issue just for completeness.
> >> > > > > >>
> >> > > > > >> Thank you,
> >> > > > > >> Leonardo
> >> > > > > >>
> >> > > > > >> > library(ggbio)
> >> > > > > >> ## Removed the output, nothing out of ordinary
> >> > > > > >>
> >> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> >> > > > > >> ## Removed the output
> >> > > > > >>
> >> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> >> > > > > >> > data(genesymbol, package = "biovizBase")
> >> > > > > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"])
> >> > > > > >> Aggregating TranscriptDb...
> >> > > > > >> Parsing transcripts...
> >> > > > > >> Parsing exons...
> >> > > > > >> Parsing cds...
> >> > > > > >> Parsing utrs...
> >> > > > > >> ------exons...
> >> > > > > >> ------cdss...
> >> > > > > >> ------introns...
> >> > > > > >> ------utr...
> >> > > > > >> aggregating...
> >> > > > > >> Done
> >> > > > > >> Constructing graphics...
> >> > > > > >> Error in sapply(listData, function(Xi)
> >> > > > > >> extends(class(Xi),
> >> > > > > >> elementTypeX)) :
> >> > > > > >> error in evaluating the argument 'X' in selecting a
> >> > > > > >> method
> >> > > > > >> for
> >> > > > > >> function 'sapply': Error in unlist(range(ranges(x.n,
> >> > > > > >> ignore.strand
> >> > > > > >> =
> >> > > > > >> TRUE))) :
> >> > > > > >> error in evaluating the argument 'x' in selecting a
> >> > > > > >> method
> >> > > > > >> for
> >> > > > > >> function 'unlist': Error in .local(x, ...) : unused
> >> > > > > >> argument
> >> > > > > >> (ignore.strand = TRUE)
> >> > > > > >>
> >> > > > > >> > traceback()
> >> > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi),
> >> > > > > >> elementTypeX))
> >> > > > > >> 14: .updateCompressedList(X, lapply_CompressedList(X,
> >> > > > > >> FUN,
> >> > > > > >> ...))
> >> > > > > >> 13: endoapply(obj.lst, function(x) {
> >> > > > > >> if (!is.null( group.name )) {
> >> > > > > >> if (!group.selfish) {
> >> > > > > >> x.n <- split(x, values(x)[, group.name ])
> >> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand =
> >> > > > > >> TRUE)))
> >> > > > > >> irs.new <- resize(irs, fix = fix, width =
> >> > > > > >> width(irs) +
> >> > > > > >> extend.size)
> >> > > > > >> irs.new <- sort(irs.new)
> >> > > > > >> .lvs <- disjointBins(irs.new)
> >> > > > > >> values(x)$stepping <-
> >> > > > > >> .lvs[as.character(values(x)[,
> >> > > > > >> group.name ])]
> >> > > > > >> x
> >> > > > > >> }
> >> > > > > >> else {
> >> > > > > >> values(x)$stepping <-
> >> > > > > >> as.numeric(as.factor(values(x)[,
> >> > > > > >> group.name ]))
> >> > > > > >> x
> >> > > > > >> }
> >> > > > > >> }
> >> > > > > >> else {
> >> > > > > >> irs <- ranges(x)
> >> > > > > >> values(x)$stepping <-
> >> > > > > >> as.numeric(disjointBins(resize(irs,
> >> > > > > >> fix = "center", width = width(irs) +
> >> > > > > >> extend.size)))
> >> > > > > >> x
> >> > > > > >> }
> >> > > > > >> })
> >> > > > > >> 12: endoapply(obj.lst, function(x) {
> >> > > > > >> if (!is.null( group.name )) {
> >> > > > > >> if (!group.selfish) {
> >> > > > > >> x.n <- split(x, values(x)[, group.name ])
> >> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand =
> >> > > > > >> TRUE)))
> >> > > > > >> irs.new <- resize(irs, fix = fix, width =
> >> > > > > >> width(irs) +
> >> > > > > >> extend.size)
> >> > > > > >> irs.new <- sort(irs.new)
> >> > > > > >> .lvs <- disjointBins(irs.new)
> >> > > > > >> values(x)$stepping <-
> >> > > > > >> .lvs[as.character(values(x)[,
> >> > > > > >> group.name ])]
> >> > > > > >> x
> >> > > > > >> }
> >> > > > > >> else {
> >> > > > > >> values(x)$stepping <-
> >> > > > > >> as.numeric(as.factor(values(x)[,
> >> > > > > >> group.name ]))
> >> > > > > >> x
> >> > > > > >> }
> >> > > > > >> }
> >> > > > > >> else {
> >> > > > > >> irs <- ranges(x)
> >> > > > > >> values(x)$stepping <-
> >> > > > > >> as.numeric(disjointBins(resize(irs,
> >> > > > > >> fix = "center", width = width(irs) +
> >> > > > > >> extend.size)))
> >> > > > > >> x
> >> > > > > >> }
> >> > > > > >> })
> >> > > > > >> 11: .local(obj, ...)
> >> > > > > >> 10: addStepping(gr, group.name = "tx_id", group.selfish
> >> > > > > >> =
> >> > > > > >> FALSE,
> >> > > > > >> fix = "start", extend.size = es)
> >> > > > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish
> >> > > > > >> =
> >> > > > > >> FALSE,
> >> > > > > >> fix = "start", extend.size = es)
> >> > > > > >> 8: .local(data, ...)
> >> > > > > >> 7: (function (data, ...)
> >> > > > > >> standardGeneric("geom_alignment"))(data = <S4 object of
> >> > > > > >> class
> >> > > > > >> "TranscriptDb">,
> >> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom =
> >> > > > > >> "alignment",
> >> > > > > >> stat = "identity", names.expr = "tx_name", label =
> >> > > > > >> TRUE,
> >> > > > > >> which = <S4 object of class "GRanges">, list())
> >> > > > > >> 6: (function (data, ...)
> >> > > > > >> standardGeneric("geom_alignment"))(data = <S4 object of
> >> > > > > >> class
> >> > > > > >> "TranscriptDb">,
> >> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom =
> >> > > > > >> "alignment",
> >> > > > > >> stat = "identity", names.expr = "tx_name", label =
> >> > > > > >> TRUE,
> >> > > > > >> which = <S4 object of class "GRanges">, list())
> >> > > > > >> 5: do.call(geom_alignment, args.res)
> >> > > > > >> 4: do.call(geom_alignment, args.res)
> >> > > > > >> 3: .local(object, ...)
> >> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"])
> >> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"])
> >> > > > > >>
> >> > > > > >>
> >> > > > > >> > sessionInfo()
> >> > > > > >> R version 3.1.0 (2014-04-10)
> >> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> >> > > > > >>
> >> > > > > >> locale:
> >> > > > > >> [1]
> >> > > > > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >> > > > > >>
> >> > > > > >> attached base packages:
> >> > > > > >> [1] parallel stats graphics grDevices utils datasets
> >> > > > > >> methods base
> >> > > > > >>
> >> > > > > >> other attached packages:
> >> > > > > >> [1] XVector_0.4.0
> >> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
> >> > > > > >> GenomicFeatures_1.16.0
> >> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0
> >> > > > > >> GenomicRanges_1.16.2
> >> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3
> >> > > > > >> ggbio_1.12.0
> >> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0
> >> > > > > >>
> >> > > > > >> loaded via a namespace (and not attached):
> >> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5
> >> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0
> >> > > > > >> Biostrings_2.32.0
> >> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6
> >> > > > > >> BSgenome_1.32.0 cluster_1.15.2
> >> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7
> >> > > > > >> dichromat_2.0-0 digest_0.6.4
> >> > > > > >> [16] fail_1.2 foreach_1.4.2
> >> > > > > >> Formula_1.1-1
> >> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0
> >> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2
> >> > > > > >> Hmisc_3.14-4
> >> > > > > >> iterators_1.0.7 labeling_0.2
> >> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31
> >> > > > > >> munsell_0.4.2 plyr_1.8.1
> >> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1
> >> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2
> >> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4
> >> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2
> >> > > > > >> [41] splines_3.1.0 stats4_3.1.0
> >> > > > > >> stringr_0.6.2
> >> > > > > >> survival_2.37-7 tools_3.1.0
> >> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1
> >> > > > > >> zlibbioc_1.10.0
> >> > > > > >> >
> >> > > > > >>
> >> > > > > >
> >> > > > > >
> >> > > > > >
> >> > > > > > --
> >> > > > > > Tengfei Yin, PhD
> >> > > > > > Seven Bridges Genomics
> >> > > > > > sbgenomics.com
> >> > > > > > 625 Mt. Auburn St. Suite #208
> >> > > > > > Cambridge, MA 02138
> >> > > > > > (617) 866-0446
> >> > > > > >
> >> > > > >
> >> > > > >
> >> > > > >
> >> > > > > --
> >> > > > > Tengfei Yin, PhD
> >> > > > > Seven Bridges Genomics
> >> > > > > sbgenomics.com
> >> > > > > 625 Mt. Auburn St. Suite #208
> >> > > > > Cambridge, MA 02138
> >> > > > > (617) 866-0446
> >> > > > >
> >> > > > > [[alternative HTML version deleted]]
> >> > > > >
> >> > > > > _______________________________________________
> >> > > > > Bioconductor mailing list
> >> > > > > Bioconductor at r-project.org
> >> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > > > > Search the archives:
> >> > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> > > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > > --
> >> > > >
> >> > > >
> >> > > > Tengfei Yin, PhD
> >> > > > Seven Bridges Genomics
> >> > > > sbgenomics.com
> >> > > > 625 Mt. Auburn St. Suite #208
> >> > > > Cambridge, MA 02138
> >> > > > (617) 866- 0446
> >> > > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > --
> >> > >
> >> > >
> >> > > Tengfei Yin, PhD
> >> > > Seven Bridges Genomics
> >> > > sbgenomics.com
> >> > > 625 Mt. Auburn St. Suite #208
> >> > > Cambridge, MA 02138
> >> > > (617) 866- 0446
> >> > >
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> >
> >> >
> >> > Tengfei Yin, PhD
> >> > Seven Bridges Genomics
> >> > sbgenomics.com
> >> > 625 Mt. Auburn St. Suite #208
> >> > Cambridge, MA 02138
> >> > (617) 866- 0446
> >> >
> >
> >
> >
> >
> > --
> > Tengfei Yin, PhD
> > Seven Bridges Genomics
> > sbgenomics.com
> > 625 Mt. Auburn St. Suite #208
> > Cambridge, MA 02138
> > (617) 866-0446
>