On 16/11/2014 00:11, Michael Hannon wrote:
Greetings. I'd like to get some advice about using OpenBLAS with R, rather
than using the BLAS that comes built in to R.
That was really a topic for the R-devel list: see the posting guide.
I've tried this on my Fedora 20 system (see the appended
You could try method = pin.
Sent from my iPhone
On Nov 16, 2014, at 1:40 AM, Yunqi Zhang yqzh...@ucsd.edu wrote:
Hi William,
Thank you very much for your reply.
I did a subsampling to reduce the number of samples to ~1.8 million. It
seems to work fine except for 99th percentile
... and I would further add to David's comments that R^2 is basically
nonsense for glm's (and mostly for lm's also -- but not a topic for
further discussion here). Likelihood ratio tests are what should be
used to judge model fits for glm's -- also not a topic for further
discussion here. Consult
Thanks for the info/suggestions!
But note that it's not just a one-step, but a two step dispatching process
with respect to `...`. That is, `foo()` and `bar()` are *not* both called
directly inside `foobar()`: `foobar()` only calls `foo()` which then calls
`bar()`.
I now came up with something
On 16/11/2014, 11:42 AM, Janko Thyson wrote:
Thanks for the info/suggestions!
But note that it's not just a one-step, but a two step dispatching
process with respect to `...`. That is, `foo()` and `bar()` are *not*
both called directly inside `foobar()`: `foobar()` only calls `foo()`
which
Dear all!,
I use this code:
dds - DESeq(ddHTSeq)
res -results(dds)
#reporting
library(ReportingTools)
library(org.Hs.eg.db)
des2Report - HTMLReport(shortName ='RNAseq_analysis_DESeq2.html',title
='RNA-seq analysis of differential expression using DESeq2 ',reportDirectory =
./Reports)
Hello all,
I've been trying to do the following analysis. I have a table (T1) that
defines sizes of my datasets (~80k rows):
size
X1 1000
X2 8323
X3 58
And then I have a table (T2) of ~ 5 million significant overlaps between
datasets:
X234 X443
X323 X1
X998 X12
What I want
Dear all,
I am using the following code for simulating Heston model. I am trying to
compare skewness with respect to different Rhos, but it doesn't seem to
work. Any body can tell me what is happening? I am using Euler-Maruyama
Monte Carlo. Here is my sample code. Any hints would be really
You have some interesting ideas about what makes for improvements in parameter
interfaces. Wrapping the arguments into a list is like creating an object to
represent all of them, except that you don't have the benefits of a class to go
with that cognitive shift. And if making classes to hold
On 11/16/2014 10:25 AM, jarod...@libero.it wrote:
Dear all!,
I use this code:
dds - DESeq(ddHTSeq)
res -results(dds)
#reporting
library(ReportingTools)
library(org.Hs.eg.db)
des2Report - HTMLReport(shortName ='RNAseq_analysis_DESeq2.html',title ='RNA-seq
analysis of differential expression
Hi Roger,
Thank you for your reply. To my understanding, changing the regression method
only helps to speed up the computation, but not necessarily solve the problem
with 99th percentile that p-values for all the factors are 1.0. I wonder how I
should interpret the result for 99th percentile,
Hello All,
I have been struggling with the following analysis in package 'unmarked':
I conducted repeated 10 min point counts over one season. I have 50 sites
(100 m radius) replicated over 3 surveys, and each individual observation
(n = 1108) is recorded at discrete distance intervals (i.e.,
Hello,
I have two spatial map objects (reproducible example further down) which I
would like to overlay in R. The ESRI shapefiles were read using:
library(rgdal)
Prairie.Boundaries - readOGR(., boundaries)
watersheds-readOGR(.,watersheds)
The two objects have same projection:
@Duncan, @Jeff: thanks for giving me your opinions, I really appreciate
that! I'm not saying that this is something that should *generally* be used
and I perfectly understand your concerns. However: correct me if I'm wrong,
but actually I'm not doing much more than generalizing the idea behind
One of the great frustrations for a newbie to R is the documentation
uses the same syntax in its description as the items it is trying to
describe, a general no-no when giving language definitions. Why does the
documentation not include the equation being represented by the
function, thereby
On Nov 16, 2014, at 5:54 PM, Ernie Stokely wrote:
One of the great frustrations for a newbie to R is the documentation uses the
same syntax in its description as the items it is trying to describe, a
general no-no when giving language definitions. Why does the documentation
not include
On Nov 16, 2014 8:10 PM, Ernie Stokely wizardc...@gmail.com wrote:
One of the great frustrations for a newbie to R is the documentation uses
the same syntax in its description as the items it is trying to describe, a
general no-no when giving language definitions. Why does the documentation
not
I like to remove from a data frame rows with labels containing
certain string, e.g., sex and rating. Below is a list of the data
frame and my failed attempt to the rows. Any clues? Thanks.
out
est se t p disc
p.(Intercept) 26.430 13.605 1.943 0.053
p.sex
Try grepl() to do pattern matching in strings. (%in% checks for
equality.) E.g., using your original 'out' do
out[ !grepl(sex|rating, rownames(out), ]
to get all but the rows whose names contain the character sequences
sex or rating.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Sun, Nov
Thank you Bill and Dennis. grepl worked great.
However, for reason I am not figuring out, the
code worked as I included the procedure
(subroutine) with a source command, viz.,
source(z:\\R\\mylib\\me.R)
Compiling the routine into a library/package, as
I always do, then the command got
Not clear what you did. Is this an example of FAQ 7.16?
---
Jeff NewmillerThe . . Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go...
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