Hi Malcolm,
In general I have found ensembl to be really great and I expect that
their gtf files are probably fine. Usually the exon rank is the 1st
thing you will see left out when a gtf file is cutting corners, and you
are correct that they seem to be including that. I ran the one for Homo
Hi,
Seems like there was some kind of billing snafu and the people that we
pay for our internal bug tracker did not receive our payment. They are
going to shut down the tracker on Monday. I'm trying to resolve this
but wanted to send a warning...any bugs you filed in the tracker may
become
My apologies, this email was not meant to go to this list.
Dan
On Sat, Feb 9, 2013 at 9:30 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi,
Seems like there was some kind of billing snafu and the people that we
pay for our internal bug tracker did not receive our payment. They are
going to
This seems related also. Using match.call to capture ... arguments returns
odd results for missing arguments. Compare against another method of
capturing ... expressions:
capture_subst - function(...) eval(substitute(alist(...)))
capture_match - function(...) match.call(expand.dots=FALSE)$...
f1
Dear R-devel-list,
Since I had no answer on the R-help-list
(http://permalink.gmane.org/gmane.comp.lang.r.general/284539) I try to
present my trouble on the R-devel-list. I am sure in the past (one year
ago) to succeed in putting accentuated characters in the \title tag in a
.Rd file.
Thanks for bringing this up, Frank.
Since many of us are educators, I'd like to suggest a bolder approach.
Discontinue even offering the stars as an option. Sadly, we can't stop
reporting p-values, as the world expects them, but does R need to cater
to that attitude by offering star display?
See Writing R Extensions:
Since R version 2.12.0 markup has been supported in the text, but use
of characters other than English text and punctuation (e.g., ‘’) may
limit portability.
So the answer is: Don't do that.
Best,
Uwe Ligges
On 09.02.2013 19:27, LaurentRdevel wrote:
Dear
Changing the default for show.signif.stars should be sufficient to ensure
that, if people are going to get themselves into trouble, they will have to
do it on purpose. It's just a visual cue; removing it will not remove the
underlying issue, namely blind acceptance of unlikely null models and
To clarify, I favor changing the defaults for stringsAsFactors and
show.signif.stars to FALSE in R-3.0.0, and view any attempt to remove
either functionality as a seemingly simple but fundamentally misguided idea.
This is just my opinion, of course. The change could easily be accompanied
by a
I appreciate Tim's comments.
I myself have a social science paper coming out soon in which I felt
forced to use p-values, given their ubiquity. However, I also told
readers of the paper that confidence intervals are much more informative
and I do provide them. As I said earlier, there is no
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