Re: [Rd] Update copyright year in manuals

[Martin Maechler]

> On Thu, Feb 23, 2017 at 03:23:10PM +0100, Martin Maechler wrote:
> > > Mikko Korpela 
> > > on Thu, 23 Feb 2017 14:02:58 +0200 writes:
> > 
> > > With new R releases soon to come, I suggest updating the
> > > Rcopyright macro in "doc/manual/R-defs.texi" to use year
> > > 2017.
> > 
> > Now this is an e-mail that *REALLY* does not fit to the R-devel
> > mailing list ... even though it is very very slightly related to
> > the R sources.
> > 
> > We do *not* want noise on R-devel, please.
> > 
> > (and let's continue this issue in private if you want)
> > Martin

> Martin, I'm confused. Should Mikko have sent his suggestion to the
> bugtracker, or just left it to the R Core Team to figure out for
> themselves? Are we not grateful for valid suggestions? What's the
> lesson here? Maybe I'm the only slow one on the list, but to me your
> reply would have been a bit more helpful if it told us what to do, not
> just what not to do...

Well, I really basically meant to do "nothing".

Mikko and I had continued the conversation in private, but here
is an excerpt of what I wrote to him:

 I think this is a case you should not even have reported at all,
 because
 
 - it is really not important: AFAIK, if you have
   copyright, the updating to new years is not important for legal
   reasons, but only for "propaganda".
 
 - (==> ) We don't ever update copyrights if we don't change the document,
   and even then do it often but not always.
 
 - more importantly: We don't clutter the SCM log files by *only*
   just changing such dates.  Some (even most?) of us, do update
   the copyright, if we do some real (non-trivial) change to the document,
   *and* notice that the last copyright is smaller than the
   current year.

I also told him that yes indeed we are grateful to learn about
errors including typos in manuals ambigous statements there, etc.

Note that sometimes even these may not need to go to R-devel
(with its 1000's of  subscribers rather interested into the
development of R, future features, bug fixes or changes of R..)
and rather be reported to R core or individuals whom you may have
identified (via svn logs) as working with these documents recently.

Martin

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[Bioc-devel] reusing topGO objects

[Lluís Revilla]

Dear Adrian and all

I am using the package topGO and I would like to know if you could help me
to reuse the same object to perform several test, see the examples below:

library("topGO")
data(GOdata)
geneSelectionFun(GOdata) <- function(x) {x == 1L}
GOdata
resultKS.elim <- runTest(GOdata, algorithm = "elim", statistic = "ks")
allRes1 <- GenTable(GOdata, resultKS.elim)
geneSelectionFun(GOdata) <- function(x) {x > 0.5}
GOdata
resultKS.elim2 <- runTest(GOdata, algorithm = "elim", statistic = "ks")
allRes2 <- GenTable(GOdata, resultKS.elim2)
ontology(GOdata) <- "CC"
resultKS.elim3 <- runTest(GOdata, algorithm = "elim", statistic = "ks")
allRes3 <- GenTable(GOdata, resultKS.elim3)
all.equal(score(resultKS.elim), score(resultKS.elim2)) # Shouldn't it be
different?

all(names(score(resultKS.elim3)) == names(score(resultKS.elim2))) # Should
the GO terms be different?
sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=es_ES.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=es_ES.UTF-8LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=es_ES.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4parallel  stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
[1] topGO_2.26.0 SparseM_1.74 GO.db_3.4.0
[4] AnnotationDbi_1.36.2 IRanges_2.8.1S4Vectors_0.12.1
[7] Biobase_2.34.0   graph_1.52.0 BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.9matrixStats_0.51.0 lattice_0.20-34
digest_0.6.12
[5] grid_3.3.2 DBI_0.5-1  RSQLite_1.1-2
tools_3.3.2
[9] memoise_1.0.0


The object GOdata have different number of "Significant" genes annotated
when I change the geneSelectionFun, thus I would expect different p-values
but there are the same p-values in allRes2 and allRes1.

Also the test on the cellular component returns the same genes ontologies
as the previous test, which should be different because it is performed in
a different GO subcategory. Maybe that's the reason why the Term column is
NA.

I am doing something wrong? How can I reuse the same object with different
tests?

Thanks your help


Lluís

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