this be easily fixed in the existing AMI? (I mean, can one just
run a 'chown' and save it as a new AMI?) If so, this might be useful.
Thanks
Simon
--
| Dr. Simon Anders, Dipl.-Phys.
| Group Leader, Institute for Molecular Medicine Finland (FIMM)
| https://www.fimm.fi/en/research/groups/anders
Hi Hervé, Martin, Wolfgang, and anybody else who might be interested
this post is stimulated by a discussion Martin Morgan and I had last
week at the CSAMA course. It is on how to improve in Bioconductor the
handling of large genomics data files like GFF or BED files with many
millions of lines.
Hi
My two cents:
On 04/06/15 19:50, James W. MacDonald wrote:
In other words, for me it is a common practice to do something like this:
fit - lmFit(eset, design)
fit2 - eBayes(fit)
gns - select(chippackage, featureNames(eset), c(ENTREZID,SYMBOL))
gns - gns[!duplicated(gns[,1]),]
fit2$genes -
Hi Martin
On 09/06/15 15:35, Martin Morgan wrote:
In case you missed it in Marc's reply, and acknowledging that this is
different from your suggestion, there is mapIds() for doing this on a
single column basis, which is the common use case where one doesn't care
too much about multiple mapping
Hi Michael
On 06/04/14 23:32, Michael Lawrence wrote:
On an arbitrary vector, the names do not need to be unique, but they DO
need to be unique on a DataFrame (according to the data.frame
conventions). Conditioning on whether there are duplicate names would be
too complicated, so it is left
Hi
On 05/04/14 17:39, Simon Anders wrote:
When I use mcols on a SummerizedExperiment object, I get a DataFrame
with the row metadata, but without rownames. This is quite annoying if I
want to select specific rows using my feature identifiers.
Okay, I should have read the help page for mcols
Hi Martin
good to see that Herve agrees with me, and I reiterate my point, because
I consider this issue very important.
The average user does _not_ expect that a function like 'biocLite',
which has the express purpose of downloading and installing packages,
does not pull the newest
(and not attached):
[1] tools_2.12.0
+---
| Dr. Simon Anders, Dipl.-Phys.
| European Molecular Biology Laboratory (EMBL), Heidelberg
| office phone +49-6221-387-8632
| preferred (permanent) e-mail: sand...@fs.tum.de
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of an unnecessary compiler warning.
Cheers
Simon
+---
| Dr. Simon Anders, Dipl.-Phys.
| European Molecular Biology Laboratory (EMBL), Heidelberg
| office phone +49-6221-387-8632
| preferred (permanent) e-mail: sand...@fs.tum.de
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. Simon Anders, Dipl. Phys.
| European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
| office phone +44-1223-492680, mobile phone +44-7505-841692
| preferred (permanent) e-mail: sand...@fs.tum.de
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Hi
please disregard the previous mail; I realized that my conclusion that
the bug is in R and not in Rpy2, was quite wrong, as I just noticed
after abit more thinking. The problem is at a pretty obvious place in
RPy2's initialization routine. I'll ask the RPy2 mailing list for help.
Simon
.
Could we not set up a Windows timer that dispatches a message to the main
thread's event handler peridoically to trigger a polling of the Gtk event
loop?]
Simon
+---
| Dr. Simon Anders, Dipl. Phys.
| European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
| office phone +44-1223-494478
(args), 0)));
34break;
35 default:
36Rprintf([%d] '%s' R type\n, i+1, name);
37 }
38}
39return(R_NilValue);
40 }
41
Best regards
Simon Anders
+---
| Dr. Simon Anders, Dipl. Phys.
| European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
| office phone +44
when this macro is defined, without even pointing out
this requirement. I merely wanted to suggest adding a little note to the
manual at this point to make the matter easier for the reader.
Best regards
Simon Anders
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Anders
+---
| Dr. Simon Anders, Dipl. Phys.
| European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
| office phone +44-1223-494478, mobile phone +44-7505-841692
| preferred (permanent) e-mail: [EMAIL PROTECTED]
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