Hi Val,
On 03/11/2014 08:57 PM, Valerie Obenchain wrote:
Hi,
On 03/11/14 15:33, Hervé Pagès wrote:
On 03/11/2014 02:52 PM, Hervé Pagès wrote:
On 03/11/2014 09:57 AM, Valerie Obenchain wrote:
Hi Herve,
On 03/10/2014 10:31 PM, Hervé Pagès wrote:
Hi Val,
I think it would help understand the
Hi Hervé
It works great. Thanks for optimizing the function, it will be very
helpful when processing larger data sets.
Best wishes
Leonard
On Fri, Mar 7, 2014 at 8:49 AM, Hervé Pagès hpa...@fhcrc.org wrote:
Hi Leonard,
Sorry for the delay. I finally managed to spend some time optimizing
Hi Laurent, Martin,
thank you for bringing this up! As pointed out by Martin, currently
the 'helvet' package gets overridden by Sweave, so this setting
affects only the knitr output.
My feeling is that the default font style should be the same
regardless of the engine used. Too keep thing
Hi Laurent, Martin,
thank you for bringing this up! As pointed out by Martin, currently
the 'helvet' package gets overridden by Sweave, so this setting
affects only the knitr output.
My feeling is that the default font style should be the same
regardless of the engine used. Too keep thing
On Tue, Mar 11, 2014 at 11:29 PM, Hervé Pagès hpa...@fhcrc.org wrote:
Hi Val,
On 03/11/2014 08:57 PM, Valerie Obenchain wrote:
Hi,
On 03/11/14 15:33, Hervé Pagès wrote:
On 03/11/2014 02:52 PM, Hervé Pagès wrote:
On 03/11/2014 09:57 AM, Valerie Obenchain wrote:
Hi Herve,
On
Should we then just drop \RequirePackage{helvet} from BiocStyle?
Cheers,
Andrzej
On Wed, Mar 12, 2014 at 3:27 PM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
Whatever we choose, we should discourage the use of other fonts: one of the
advantages of bioc style is to make it easy to
Should we then just drop \RequirePackage{helvet} from BiocStyle?
That seems a reasonable solution to me.
Laurent
Cheers,
Andrzej
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
On 03/12/2014 08:18 AM, Laurent Gatto wrote:
Should we then just drop \RequirePackage{helvet} from BiocStyle?
That seems a reasonable solution to me.
yep! Martin
Laurent
Cheers,
Andrzej
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box
Dear all,
I have an error using the select function from the AnnotationDbi package.
I try to convert some geneID into Symbol, but for some strange reasons it
crashed.
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb - TxDb.Hsapiens.UCSC.hg19.knownGene
isActiveSeq(txdb)[seqlevels(txdb)] - FALSE
Hi Nicolas,
On 3/12/2014 12:39 PM, Servant Nicolas wrote:
Dear all,
I have an error using the select function from the AnnotationDbi package.
I try to convert some geneID into Symbol, but for some strange reasons it
crashed.
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb -
Hi Martin, Mike
a DESeq2 user brought up the observation that when he subsets a ‘DESeqDataSet’
object (the class inherits from ‘SummarizedExperiment’) by samples, he often
ends up with unused factor levels in the colData. (Esp. since the subsetting is
often to select certain subgroups). Would
Also,
There is nothing wrong with using GENEID the way that you initially
did. It was just a small bug that prevented some internal subsetting
from working properly and that is now fixed.
It just happened that GENEID was equivalent to ENTREZID in this case.
And that ends up making it a
I would prefer the droplevels method for SummarizedExperiment, since
this is consistent with the use of droplevels on data.frame objects.
On Wed 12 Mar 2014 03:02:37 PM PDT, Wolfgang Huber wrote:
Hi Martin, Mike
a DESeq2 user brought up the observation that when he subsets a ‘DESeqDataSet’
On 03/12/2014 03:02 PM, Wolfgang Huber wrote:
Hi Martin, Mike
a DESeq2 user brought up the observation that when he subsets a ‘DESeqDataSet’
object (the class inherits from ‘SummarizedExperiment’) by samples, he often
ends up with unused factor levels in the colData. (Esp. since the
On Wed, Mar 12, 2014 at 3:45 PM, Martin Morgan mtmor...@fhcrc.org wrote:
On 03/12/2014 03:02 PM, Wolfgang Huber wrote:
Hi Martin, Mike
a DESeq2 user brought up the observation that when he subsets a
'DESeqDataSet' object (the class inherits from 'SummarizedExperiment') by
samples, he often
On Wed, Mar 12, 2014 at 3:52 PM, Michael Lawrence
lawrence.mich...@gene.com wrote:
On Wed, Mar 12, 2014 at 3:45 PM, Martin Morgan mtmor...@fhcrc.org wrote:
On 03/12/2014 03:02 PM, Wolfgang Huber wrote:
Hi Martin, Mike
a DESeq2 user brought up the observation that when he subsets a
At the least, I will add the use of droplevels on colData to the vignette.
On Mar 12, 2014 7:28 PM, Steve Lianoglou lianoglou.st...@gene.com wrote:
On Wed, Mar 12, 2014 at 3:52 PM, Michael Lawrence
lawrence.mich...@gene.com wrote:
On Wed, Mar 12, 2014 at 3:45 PM, Martin Morgan
Can anyone help me understand how I got 2 versions of the same library
loaded, how to prevent it, and what the consequences are? Running under
Debian GNU/Linux squeeze.
lsof and /proc/xxx/map both show 2 copies of several libraries loaded:
/home/ross/install/lib/libmpi.so.1.3.0
Ross,
On Mar 12, 2014, at 5:34 PM, Ross Boylan r...@biostat.ucsf.edu wrote:
Can anyone help me understand how I got 2 versions of the same library
loaded, how to prevent it, and what the consequences are? Running under
Debian GNU/Linux squeeze.
lsof and /proc/xxx/map both show 2 copies of
Comments/questions interspersed below.
On Wed, 2014-03-12 at 22:50 -0400, Simon Urbanek wrote:
Ross,
On Mar 12, 2014, at 5:34 PM, Ross Boylan r...@biostat.ucsf.edu wrote:
Can anyone help me understand how I got 2 versions of the same library
loaded, how to prevent it, and what the
20 matches
Mail list logo
