h my old address 'sand...@fs.tum.de',
which I still have access to.
For authentication, this e-mail is signed, with the signature verified
by the Géant CA. (Géant is the organisation running the European
academic internet backbone.)
Thanks and best regards
Simon
+---
| Pro
oot.
Can 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/
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 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
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(, featureNames(eset), c("ENTREZID","SYMBOL"))
gns <- gns[!duplicated(gns[,1]),]
fit2$genes <- gns
Hi Jarod
Mike overlooked one point in your question
On 11/07/14 12:05, jarod...@libero.it wrote:
If I interested in the genes that have a foldchange more than 0.5 and 2 I need
to use this comand is it right?
DESeq2 reports al fold changes on a log2 scale. So your limits of 0.5
and 2 for unlo
Hi
> This is because an
> SE is modeled as a matrix, which does not have the same constraint as a
> data.frame.
Thanks, Michael. That's the point I was missing. I never realized that
array dimnames don't have to be unique. Strange, actually.
Simon
_
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 lef
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 rea
Hi Martin et al.
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.
Would it be possible to change that?
Simon
Demonstration of the issue:
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 package.
Hi
On 19/06/13 23:44, Martin Morgan wrote:
As a message (not warning or error), how about
New features are available in Bioconductor version 2.12, R version
3.0.1.
See http://bioconductor.org/install
and if the instructions / dire consequences at
http://bioconductor.org/install are not s
Hi
I would like to suggest the floowing change to the biocLite.R script: As
soon as it is sourced, it should check whether the R interpreter it is
running in has at least the current major version number, and if not,
display a conspicious warning such as
"WARNING: You are not using a current
Hi
a user just alerted me that no binary packages for Mac are being built
for my package "HilbertVis".
I have some recollection that somebody took it out of the build manifest
a while ago, beacuse it depends on EBImage, and EBImage was unavailable
for Mac for a while due to all these problem
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