Thanks Dan and Martin for the advice.
It's interesting that this doesn't seem to have come up much before given
our shared obsession with reproducible analyses - I'm sure you'd agree that
(eg) any third party source update should mean a new, explicit dependency
chain for a pipeline - truly
Hej Bioc Core!
There was some discussion last year about implementing a BamStreamer (à la
FastqStreamer), but I haven't seen anything like it in the current devel. I've
implemented the following function that should do the job for me - I have many
very large files, and I need to use a cluster
Ross,
Reproducibility is extremely important (I do work on that subject myself),
but I do hope you will be splashing some sort of warning along the lines of
This analysis was run using BioConductor package XXX v Y.Y.Y which
required an out of cycle bug fix. Such out of cycle fixes often indicate
Note the final s in assays. It is super slow. This is a BSseq object
with 28M rows and 7 columns, which means there are two assays M and Cov
each being 28M x 7 (which is pretty big, on the Gb scale)
These two commands retrieve the same data as far as I understand.
Additional question, simplified:
Assuming I have matrices M and Cov and I want to create a
SummarizedExperiment around them. What is the most efficient (least
copying) way of doing this. Currently I use
assays = SimpleList(M = M, Cov = Cov)
SummarizedExperiment(assays = assays, rowData,
The problem is that the dimnames are stored in only one location, and this is
not on the assays. When you ask for the assays, the dimnames are added,
triggering a full copy of the data. If the dimnames are not of interest, then
assays(BS, withDimnames=FALSE)
This is not really ideal, so I'll
Greetings DESeq2ers,
I've been playing around with different ways to encode a 2x2 factorial
design I'm working with: 4 cell types, 4 treatments and exploring
what's cooking in there.
I thought that the nested interaction formula used in the limma user's
guide (section 8.5.3) would be an easy way
This is side-stepping the question, but I am not aware that it ever makes
sense to include the A:B term in a design matrix without also including
the main effects of A and B (here I include obvious extensions such as A +
A:B + C where B is a coarser factor than C, so here the main effects of B
are
Hi Kasper,
On Tue, Jul 9, 2013 at 5:51 PM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
This is side-stepping the question, but I am not aware that it ever makes
sense to include the A:B term in a design matrix without also including
the main effects of A and B (here I include
Actually the limma guide is right and I am wrong. For a moment I forgot
the precise meaning of : in context of R's formula system.
You still need to be careful with this, as the limma guide also states
quite clearly.
Kasper
On Tue, Jul 9, 2013 at 9:01 PM, Steve Lianoglou
seconded
On Tue, Jul 9, 2013 at 6:33 PM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
Especially since it seems that
assay()
has no option for dim names and therefore automatically removes them.
I vore for withDimNames = FALSE and also adding the option to assay() (or
I am trying to write S4 methods with difftime in the signature but
am being informed (? not a warning or error) that difftime is not
a class. Nevertheless, dispatch takes place. Should I simply ignore
that information? Here is a toy example:
setClass(foo, contains = Date)
setMethod(+, c(foo,
difftime is an S3 class, not an S4 class. To convert it, include the line
setOldClass(difftime)
and the setMethod call should work.
On 7/9/2013 6:03 AM, Dan Murphy wrote:
I am trying to write S4 methods with difftime in the signature but
am being informed (? not a warning or error) that
In running the following example of a loglinear model for the Titanic data,
I was surprised to see NaN reported for the
Pearson chisq
loglin(Titanic, margin=list(1:3, 4))
2 iterations: deviation 2.273737e-13
$lrt
[1] 671.9622
$pearson
[1] NaN
$df
[1] 15
$margin
$margin[[1]]
[1] Class Sex
On Sat, Jun 15, 2013 at 4:38 PM, Simon Urbanek
simon.urba...@r-project.org wrote:
On Jun 15, 2013, at 2:42 PM, Martin Maechler wrote:
Dirk Eddelbuettel e...@debian.org
on Sat, 15 Jun 2013 10:45:04 -0500 writes:
On 15 June 2013 at 07:00, Dirk Eddelbuettel wrote:
|
| On 15 June 2013 at
Hi Dan,
On 9 July 2013 at 19:52, Dan Tenenbaum wrote:
| Picking up a somewhat old thread...what is the final status of this?
In r-patched and r-devel, check the NEWS file.
| It doesn't look like an option was added to control the permissions of
| installed package files.
| It also seems that
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