On Tue, Jul 1, 2014 at 1:27 PM, Erin Hodgess erinm.hodg...@gmail.com wrote:
Hello R People:
I'm having a forest/trees location problem with the output of nls.
If I save the output to an object, and print the object, it shows, amongst
other things, the residual sum of squares. I would like
Not sure if this is better than your brute force and you may be able
to simplify it...
notStart = function(x)
{
n = length(x)
i0 = which(x);
n0 = length(i0);
i0!=c(1:n)[1:n0];
}
notStartNorEnd = function(x) { which(x)[notStart(x) rev(notStart(rev(x)))] }
notStartNorEnd(c(F, F, F))
Hi Pan,
On Wed, May 14, 2014 at 9:14 PM, Panos Bolan panbo...@hotmail.com wrote:
Dear list,
Apologies for posting this to both Bioconductor and here. I recently read a
Bioconductor post where the developer of the WGCNA suggested the use of the
package for RNA-seq data analysis after
WGCNA maintainer here. When working with a large data set, you have a
few options.
1. Without being snarky, the best option is to get (or get access to)
a computer with large-enough RAM. Many universities, departments, and
other research institutes have computer clusters with nodes with at
least
Make sure you have cairo-devel installed, and remove the lines
export CAIRO_LIBS=${HOME}/usr/local/lib
export CAIRO_CFLAGS=${HOME}/usr/local/include
from your .bashrc file. If you have cairo-devel installed normally,
the headers should be found with default settings of all search paths.
The
HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_STRING_H 1
| #define HAVE_SYS_TIME_H 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h. */
On Mon, Apr 28, 2014 at 7:50 PM, Peter Langfelder
peter.langfel...@gmail.com wrote:
On Mon, Apr 28, 2014 at 7:14 PM, Fong Chun Chan fongchunc
You are using the wrong algorithm. You want Partitioning around
Medoids (PAM, function pam), not k-means. PAM is also known as
k-medoids, which is where the confusion may come from.
use
library(cluster)
cl = pam(dis, 4)
and see if you get what you want.
HTH,
Peter
On Mon, Apr 28, 2014 at
On Fri, Apr 25, 2014 at 6:35 PM, chris Jhon cjhon...@gmail.com wrote:
Hi,
I am using hclust and cutree to cluster a data frame y and cut it into few
clusters as follows
y
V1 V2 V3 V4
A 1 2 3 4
B 5 6 7 8
C 9 10 11 12
D 13 14 15 16
E 17 18 19 20
On Wed, Apr 9, 2014 at 11:27 AM, Cassiano dos Santos crn...@gmail.com wrote:
I am testing a call to a C function from R, using .C interface. The test
consists in passing a numeric vector to the C function with no entries,
dynamically allocates n positions, makes attributions and return the
On Sat, Feb 15, 2014 at 8:43 AM, Lorenzo Isella
lorenzo.ise...@gmail.com wrote:
Dear All,
I am a bit puzzled.
I am developing a random forest model.
The data is large and it involves hundred of predictors, but the code I have
written is relatively simple.
After training my random forest
In short, use dplyr::summarize or plyr::summarize to select the one you want.
HTH,
Peter
On Wed, Jan 29, 2014 at 2:19 PM, Trevor Davies davies.tre...@gmail.com wrote:
I think I have a hole in my understanding of how R uses packages (or at
least how it gives functions in packages priority). I
Here's a solution:
# This gives a vector of counts (if z is a data frame, first convert
it to a matrix)
res = sapply(as.vector(z), function(x) sum(w==x))
# This copies the dimensions of the variable 'z' to 'res':
dim(res) = dim(z)
Peter
On Thu, Jan 23, 2014 at 7:43 AM, m.beza...@lse.ac.uk
On Sat, Dec 28, 2013 at 7:27 PM, Andrew Hoerner ahoer...@rprogress.org wrote:
Let us suppose that we have a function foo(X) which is called inside
another function, bar(). Suppose, moreover, that the name X has been
assigned a value when foo is called:
X - 2
bar(X=X){
foo(X)
}
I have
On Thu, Dec 12, 2013 at 3:09 PM, capricy gao capri...@yahoo.com wrote:
I could not figure out what was the default when I ran hclust() without
specifying the method.
According to help(hclust), the default method is complete linkage.
HTH,
Peter
__
On Tue, Dec 10, 2013 at 6:55 PM, bakerwl bake...@uwyo.edu wrote:
Expected values are needed to test a null hypothesis against observed
counts, but if total observed counts are 20 for 3 categories, then a null
hypothesis of a random effect would use expected values = 6.67 in each of
the 3
On Mon, Dec 9, 2013 at 2:08 PM, Katharine Miller - NOAA Federal
katharine.mil...@noaa.gov wrote:
Hello,
I am having difficulty obtaining the correct colors in my R charts.
colors()[c(552, 254, 26)]
[1] red green blue
But, if I specify col=552 in my barplot, I get gray bars. Likewise,
On Tue, Nov 5, 2013 at 3:36 PM, Uwe Ligges
lig...@statistik.tu-dortmund.de wrote:
On 06.11.2013 00:26, Simon Pickert wrote:
Mcapply from package 'parallel'. Also see package 'multicore'
Not mcapply: it won't work under Windows that the OP asked for.
But package parallel is the right
Joshua,
I'm not sure I understand your aim correctly, but if I do, here's my
advice: If you are able to find the clusters according to rows or
columns using clustering, you must be using some kind of a distance
matrix that encodes whether two antibodies should be in one bin for
rows, and a
One more question about avoiding copies when modifying lists. I would
like to call a function (call it 'f') that does an operation on a
large array according to a given index. For example
f = function(data, index) sum(data[index])
The idea is to repeatedly call f() with the same 'data' but
I am not an expert on shrinkage estimators of partial correlations
(such as the one in corpcor), but my sense is that it is difficult to
provide a good estimate of a p-value. You could try to email the
authors of the package and ask them, but this may be more of a
statistics rather than R
Disclaimer: I haven't seen your tif file and I know nothing about
readTiff... but here go some general comments.
TIF files can use different bit depths (number of bits to store each
pixel (or each color for each pixel). Most common software outputs 8-
or 16-bits, but your file probably has a
On Thu, Jul 25, 2013 at 9:30 AM, Richard M. Heiberger r...@temple.edu wrote:
On Vista with Powerpoint 2007, file2.eps crashes powerpoint,
Once file.eps displayed, several times it crashed powerpoint.
My task is now to see if ghostscript can read a pdf or ps or eps and
convert it to png at
[cc-ing the list]
On Wed, Jul 10, 2013 at 11:36 PM, Christofer Bogaso
bogaso.christo...@gmail.com wrote:
Hello again,
I was wondering if it is possible to install OpenBLAS linear algebra
library in R running under windows.
You will have to re-compile R from source and re-install it.
You have several options. You can use theF18 package manager to
install R directly from a Fedora software repository but the R may be
slightly out of date (IIRC Fedora 19 provides R-3.0.0; not sure about
F18).
Or, on your CRAN mirror page, ignore the Download and install R
section and go
On Mon, Apr 22, 2013 at 1:15 PM, Barbour, Russell
russell.barb...@yale.edu wrote:
I am having a problem with loading R on my 64 bit computer. It used to
load perfectly until I upgraded to R 3.0.0 now it takes about 10 to even
20 minutes ? Does anyone know how to remedy this problem?
On Wed, Apr 17, 2013 at 10:36 AM, R. Michael Weylandt
michael.weyla...@gmail.com
It sounds like you want .Deprecate
?.Deprecate
Perhaps you meant Deprecated?
?Deprecated
Best,
Peter
__
R-help@r-project.org mailing list
On Wed, Mar 6, 2013 at 4:18 PM, Yao He yao.h.1...@gmail.com wrote:
Dear all:
I have a big data file of 6 columns and 6 rows like that:
AA AC AA AA ...AT
CC CC CT CT...TC
..
.
I want to transpose it and the output is a new
On Tue, Feb 26, 2013 at 8:34 AM, Joanna Papakonstantinou
joanna.p...@gmail.com wrote:
So I realized I had to convert my dd.daisy to a matrix and used:
ddmatrix.daisy-as.matrix(dd.daisy)
and then I passed that in as the distM:
cutreeDynamic(as.hclust(dd.diana), cutHeight = NULL, minClusterSize
On Thu, Jan 31, 2013 at 3:55 PM, Rich Shepard rshep...@appl-ecosys.com wrote:
I don't see what's missing in my statements to add rows to a data frame
and someone else will probably see what needs to be added to the statements.
The data frame has this structure (without any data):
$
Do your lines start with the hash mark #? If so, they are considered
comment. Set comment.char= in your call to read.csv. Another
frequent culprit (personal experience) are apostrophes ('). If you
have any in your file, use the argument quote = \ or, if you are
sure the data are not quoted, use
On Thu, Jan 17, 2013 at 4:57 AM, vaseem shaikh vsma...@gmail.com wrote:
But still, i am also trying to install the package by locally giving
absolute path with repos= Null and type = Source, will CRAN have any role
to play here???
To compile a package on Windows, you need to install R tools
:41 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote:
On 13-01-03 7:01 PM, Peter Langfelder wrote:
Hello all,
I am running into a problem with garbage collection not being able to
free up all memory. Unfortunately I am unable to provide a minimal
self-contained example, although I can provide
On Tue, Dec 4, 2012 at 11:27 AM, Charles Novaes de Santana
charles.sant...@gmail.com wrote:
Dear Michael,
Thank you for your answer.
I have 2 matrices. Each position of the matrices is a weight. And I
need to calculate the following sum of differences:
Considering:
mat1 and mat2 - two
On Mon, Dec 3, 2012 at 3:30 PM, tdbuskirk trent.busk...@nielsen.com wrote:
Hello R Gurus,
I am perplexed by the different results I obtained when I ran code like
this:
set.seed(100)
test1-randomForest(BinaryY~., data=Xvars, trees=51, mtry=5, seed=200)
predict(test1,
On Fri, Nov 30, 2012 at 9:47 AM, jaybell stephe...@yahoo.com.tw wrote:
a=c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9)
b=c(0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1)
cor(a,b)= -1
a'=qbinom(a, 1, 0.5)
b'=qbinom(b, 1, 0.5)
why cor(a',b') becomes -0.5 ?
On my computer the correlation is
Not tested but should work:
sums = tapply(x, group, sum);
sums.ext = sums[ match(group, names(sums))]
normalized = x/sums.ext
It may be that the tapply is just as slow as your loop though, I'm not sure.
HTH,
Peter
On Thu, Nov 29, 2012 at 10:55 AM, Noah Silverman noahsilver...@ucla.edu wrote:
On Wed, Nov 28, 2012 at 4:44 PM, Shi, Tao shida...@yahoo.com wrote:
Hi list,
I've encounter this problem (see below). I know it's particularly R-related
and it's easy to get by but it still bothers me a lot.
It looks the last character of N.C. is a space to me, but it's clearly
not.
On Thu, Nov 15, 2012 at 5:48 PM, Benjamin Ward (ENV) b.w...@uea.ac.uk wrote:
Hi,
I have some values in a list format generated by the following:
Path_Number - 0010
ID.Path - formatC(0001:Path_Number, width=4, flag=0) # Make vector of ID's.
No_of_Effectors - sample(1:550, length(ID.Path),
On Thu, Nov 1, 2012 at 10:28 AM, Hermann Norpois
hnorp...@googlemail.com wrote:
Hello,
my data is sorted by start.ens (see below). And now I would like to extract
all rows (so called* defined row*s) with type==Expression - subset (df,
type==Expression) - and the aforegoing type==DNase HS
It seems you don't quite understand how foreach works. foreach (..)
%dopar% { ... } takes the last value from each of the second {...}
evaluations and feeds them to the .combine function (in your case
rbind()). Since your last call in the %dopar% {...} block is assign(),
you are not getting
currently learning to use R, so please forgive me if there is an
obvious explanation for the following problem. My goal is to perform WGCNA
on a dataset of 19776 genes, so I opted to follow the block-wise network
construction (Section 2c) in the WGCNA R Tutorial by Peter Langfelder and
Steve
On Tue, Oct 9, 2012 at 4:37 PM, eliza botto eliza_bo...@hotmail.com wrote:
Dear useRs,
i am using NbClust to determine appropriate number of cluster for
hclustering. i am consistently getting the following error
Error in if (is.na(n) || n 65536L) stop(size cannot be NA nor exceed
65536)
Hi Eliza,
this is not __reproducible__ code - how am I supposed to know what's
wrong when I don't have the input files you use? Please read the help
for NbClust carefully and check that all your input variables have the
correct dimensions. Some of the input seems strange, for example the z
matrix
run
capabilities(what=cledit)
in your R terminal session. If you get FALSE, your R was compiled
without command line editing support which you need for the up arrow
action.
Peter
On Mon, Oct 8, 2012 at 8:04 PM, Tjun Kiat Teo teotj...@gmail.com wrote:
I am using R on Fedora 17 and the up arrow
Well, if I read the error message right, your image is too large. I
think you should explore alternate formats - does the journal accept
figures in a vector format such PS, EPS or PDF? Such figures will be
much easier to handle than a humongous tiff with file size of 60+
megabytes.
HTH,
Peter
Erin,
you seem to confuse R and C syntax a bit, among other things. See below.
On Mon, Sep 24, 2012 at 3:03 PM, Erin Hodgess erinm.hodg...@gmail.com wrote:
Dear R People:
I'm working on a project that will pass a matrix from an R function to
a C subroutine.
I tried to write the following:
Enclose the file name tmax.final.text in quotes. Otherwise R is
looking for a variable named tmax.final.text, not the file name named
tmax.final.text.
HTH
Peter
On Thu, Sep 20, 2012 at 1:02 PM, gfishel gfis...@wral.com wrote:
Thanks for your help! Unfortunately, I am now getting this:
Bert is correct that this is a statistics questions, but I'll throw in
my 2 cents anyway. The CMH test is formulated for count data and makes
certain assumptions on the distribution of the observed values. Since
you don't have count data (your data are not integer), chances are
that the
On Tue, Sep 18, 2012 at 5:35 PM, David Winsemius dwinsem...@comcast.net wrote:
On Sep 18, 2012, at 5:10 PM, John Sorkin wrote:
Window 7
R 2.15
I am writing a simulation which generates sample sized estimates from
simulated data. When I run the function shown below,
On Fri, Sep 7, 2012 at 9:04 AM, Chris82 rubenba...@gmx.de wrote:
Hey R users,
I am a little bit confused.
require(plotrix)
plot(0,xlim=c(-10,10),ylim=c(-10,10),type=n,xlab=,ylab=)
draw.circle(0,0,5)
lines(c(0,0),c(0,5))
lines(c(0,5),c(0,0))
The culprit are unequal margins. Issue
On Thu, Aug 30, 2012 at 10:48 AM, zz czh...@uams.edu wrote:
Hello,
I have a self-defined function to be computed on each column in a matrix.
The basic idea is to ignore the elements that have value of 0 during
computation.
I should be able to write my own function but it could be
Hi all,
is there a way to extract the name of a function, i.e. do the reverse
of match.fun applied to a character string? I would like to print out
the name of a function supplied to another function as an argument.
For example:
myFunc = function(x) { x+1 }
applyFunc = function(fnc, x)
{
fnc
On Wed, Aug 29, 2012 at 3:36 PM, Peter Langfelder
peter.langfel...@gmail.com wrote:
Hi all,
is there a way to extract the name of a function, i.e. do the reverse
of match.fun applied to a character string? I would like to print out
the name of a function supplied to another function
On Wed, Aug 29, 2012 at 4:14 PM, William Dunlap wdun...@tibco.com wrote:
deparse(substitute(fnc)) will get you part way there.
...
I like to let the user override what substitute might say by
making a new argument out of it:
applyFunc(function(x)x*10, 1:3)
fnc is function(x) x * 10
[1] 10 20
On Fri, Aug 17, 2012 at 11:34 AM, Rui Barradas ruipbarra...@sapo.pt wrote:
Hello,
No, factors may use less memory. System dependent?
I think it's a 32-bit vs. 64-bit distinction - I get Rui's results on
64-bit Windows and Linux installation, but Bert's result on a 32-bit
Linux machine.
Peter
On Wed, Aug 1, 2012 at 6:30 AM, Ingezz irholt...@gmail.com wrote:
Dear Peter,
I have another question about WGCNA. I am using the package for
meta-analysis to find modules preserved in several datasets. However, I am
unsure how to handle the softpower, because each dataset has its own ideal
Hi all,
I cant' wrap my head around an error from the coxph function (package
survival). Here's an example:
library(survival)
n = 100;
set.seed(1);
time = rexp(n);
event = sample(c(0,1), n, replace = TRUE)
covar = data.frame(z = rnorm(n));
model = coxph(Surv(time, event)~ . , data = covar)
R
On Thu, Jul 26, 2012 at 4:19 PM, Thomas Lumley tlum...@uw.edu wrote:
YOu need to update the survival package: from its NEWS file
Changes in version 2.36-14
A supposedly cosmetic change to coxph in the last release caused
formulas with a . on the right hand side to fail. Fix this and add a
On Fri, Jun 29, 2012 at 10:15 AM, Spencer Graves
spencer.gra...@structuremonitoring.com wrote:
Dear Prof. Ripley:
Thanks for the reply. Unfortunately, flush.console() seems to lock up
my system. I tried the following:
for(i in 1:1e7){
tst - sin(i)
if((i%%1e5)==0)cat(i, )
On Fri, Jun 15, 2012 at 8:04 AM, Ingezz irholt...@gmail.com wrote:
Dear Peter,
I am trying to apply the WGCNA meta-analysis for two (or more) microarray
datasets-tutorial to my own data.
mp=modulePreservation(multiExpr,multiColor,referenceNetworks=1,verbose=3,networkType=signed,
On Fri, Jun 8, 2012 at 10:25 AM, David Winsemius dwinsem...@comcast.net wrote:
On Jun 8, 2012, at 1:11 PM, Ben quant wrote:
Hello,
How do I change this:
cnt_str
[1] \002 \001 \102
...to this:
cnt_str
[1] 2 1 102
Having trouble because of this:
nchar(cnt_str[1])
[1] 1
\001
Hi,
not sure this is the right mailing list, but anyway - I maintain the
WGCNA package, and was just alerted by a Mac user that it is not
available. Looking at the error log at
http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/WGCNA-00check.html
reveals
checking package dependencies
On Wed, May 30, 2012 at 12:47 PM, Iain Gallagher
iaingallag...@btopenworld.com wrote:
Hi Phil
Thanks, but this still doesn't work.
Here's a reproducible example (was wrapping my head around these functions
before).
x - as.data.frame(cbind(rep('a',5), rep('b',5)))
y -
On Wed, May 30, 2012 at 4:07 PM, Chris Burns chris.bur...@gmail.com wrote:
I have a huge matrix of unspecified covariates and the corresponding sales
for them. What is the best way to predict the sales from the covariates?
Don't want to sound rude, but given your very vague problem
On Centos and most likely other RedHat/Fedora systems, gfortran is
contained in the package gcc-gfortran. Install that package before
trying to install R.
HTH,
Peter
On Sun, May 27, 2012 at 8:43 AM, ya xinxi...@163.com wrote:
Hi Rich，
You mean, the R source code package contains the FORTRAN
On Thu, May 24, 2012 at 9:31 AM, r-help.20.tre...@spamgourmet.com wrote:
Dear R-Help,
I have a clustering problem with hclust that I hope someone can help
me with. Consider the classic hclust example:
hc - hclust(dist(USArrests), ave)
plot(hc)
I would like to cut the tree up in
On Mon, Apr 30, 2012 at 12:34 PM, Zeeberg, Barry (NIH/NCI) [E]
zeebe...@mail.nih.gov wrote:
I am creating a package, and a rather long usage line for one function
becomes truncated in the generated .pdf manual. Is there a way that I can
prevent that truncation?
How long is rather long? In
On Tue, Apr 24, 2012 at 3:05 PM, Rich Shepard rshep...@appl-ecosys.com wrote:
On Tue, 24 Apr 2012, Rich Shepard wrote:
I'll rebuild R-2.15 and start over. Will post results after doing that.
New build, new repository, same results.
Quite the new experience with R, but one I need to
On Fri, Apr 20, 2012 at 12:44 PM, Charles Determan Jr deter...@umn.edu wrote:
Greetings R users,
I have a curious problem. I read in a csv file (subset shown below) as
normal
data=read.table(C:/Users/Chaz/Desktop/test.csv,sep=,,header=TRUE,
na.strings=.)
However, the numbers from the
On Fri, Apr 20, 2012 at 2:48 PM, Ben quant ccqu...@gmail.com wrote:
Hello,
If the exact value does not exist in the vector, can I still get at the
intersections? Is there a simple way to do this and avoid looping? Seems
like there would be a simple R function to do this...
Example:
vec -
On Wed, Apr 18, 2012 at 7:25 PM, chuck.01 charliethebrow...@gmail.com wrote:
Let say I have an object (I hope my terminology is correct) a
a - 12
a
[1] 12
And a has been assigned the number 12, or whatever
And lets say I have a character call_A
call_A - a
call_A
[1] a
What is the
On Tue, Apr 3, 2012 at 2:41 AM, vinod1 vinod.hegd...@gmail.com wrote:
Sarah,
. clust_tree=hclust(as.dist(x),method=complete)
. plot(clust_tree)
this produces a dendrogram, whereas
. clust_tree=hclust(as.dist(x),method=complete)
. cut = cutree(clust_tree,k=1:5)
.
On Tue, Apr 3, 2012 at 7:21 AM, email mail email8...@gmail.com wrote:
Hi:
I have clustered microarray gene expression data and trying to map between
microarray probe, gene, pathway, gene ontology, and homology for a set of
(affy) microarray probes. Is there any package in R which facilitates
On Thu, Mar 29, 2012 at 3:49 PM, Benjamin Caldwell
btcaldw...@berkeley.edu wrote:
Hello,
I'm trying to create a vector of r^2 values for using a function which I
will run in a for loop. Example:
per-rnorm(100,.5,.2)^2
x-rnorm(100,10,5)
y-rnorm(100,20,5)
fr-data.frame(x,y,per)
On Thu, Mar 29, 2012 at 9:41 PM, Jim Silverton jim.silver...@gmail.com wrote:
Anyone knows how to get around this message? I am trying to update some
packages in R but I get the following message I use R for 64 bit windows.
Warning in install.packages(update[instlib == l, Package], l,
On Wed, Mar 28, 2012 at 9:09 AM, Jessica Streicher
j.streic...@micromata.de wrote:
Might not be the best place to ask, but i could get lucky..
I have setup an eclipse environment to write sweave files lately and wanted
to switch to knitr. I could get it to work on easy files, but my earlier
On Mon, Mar 19, 2012 at 2:07 PM, David Stevens david.stev...@usu.edu wrote:
I'm a bit clumsy about many things in R. Here's my problem. I'm trying to
build a square sparse matrix and populate it without looping (bad practice,
right). I have vectors of matched row/column pairs for which the
Seems you're missing the required header(s). Can't find the example in
the extensions manual but you probably need
#include Rinternals.h
or
#include Rdefines.h
HTH,
Peter
On Wed, Mar 14, 2012 at 11:03 PM, Erin Hodgess erinm.hodg...@gmail.com wrote:
Dear R People:
Here is something that I
On Thu, Mar 15, 2012 at 1:48 PM, A J anxu...@hotmail.com wrote:
Hi everybody!
Anybody knows how can I get detalied information about clusters after using
hclust?
The issue is that if I have some items in different clusters, I would like to
get the cluster where each item is placed.
Taking
On Sun, Mar 11, 2012 at 1:46 AM, Ebrahim Jahanshiri
e.jahansh...@gmail.com wrote:
Dear list,
I understand that to raise matrix A to power (-1/2) we should use something
like this:
eigen(A)$vectors%*%diag(1/sqrt(eigen(A)$values))%*%t(eigen(A)$vectors)
[from previous discussions:
On Thu, Mar 8, 2012 at 4:41 AM, Massimo Di Stefano
massimodisa...@gmail.com wrote:
Hello All,
i've a set of observations that is in the form :
a, b, c, d, e, f
67.12, 4.28, 1.7825, 30, 3, 16001
67.12, 4.28, 1.7825, 30, 3, 16001
66.57, 4.28,
On Fri, Mar 9, 2012 at 1:50 PM, Massimo Di Stefano
massimodisa...@gmail.com wrote:
Peter,
really thanks for your answer.
install.packages(flashClust)
library(flashClust)
data - read.csv('/Users/epifanio/Desktop/cluster/x.txt')
data - na.omit(data)
data - scale(data)
mydata
I don't think you can speed it up by a whole lot... but you can try a
few things, especially if you don't have missing data in the matrix
(which you probably don't). The main question is what takes most of
the time- the api calls or the cor() call? If it's cor, here's what
you can try:
1.
On Thu, Mar 1, 2012 at 12:28 PM, John C Nash nas...@uottawa.ca wrote:
Not paying close attention to detail, I entered the equivalent of
pstr-c(b1=200, b2=50, b3=0.3)
when what I wanted was
pnum-c(b1=200, b2=50, b3=0.3)
There was a list thread in 2010 that shows how to deal with un-named
Frank,
maybe I'm not understanding something right... you say right-justify
in the right margin, meaning justify against the very right edge of
the plot margin area? Since you're setting your right margin to 5, why
not just
mtext(s, side=4, las=1, at=5, adj=1, line = 5, cex=1)
mtext(s, side=4,
On Thu, Mar 1, 2012 at 8:05 PM, Ben quant ccqu...@gmail.com wrote:
Hello,
I have another question
I have a data frame that looks like this:
a b
2007-03-31 20070514 20070410
2007-06-30 20070814 20070709
2007-09-30 20071115 20071009
2007-12-31 20080213
On Mon, Feb 27, 2012 at 9:41 AM, Jannis bt_jan...@yahoo.de wrote:
Dear list members,
does anyone have an idea why the following construction does not work but
gives the following error message:
assign('test', array(1:10, dim=c(10,10)))
dimnames(get('test')) - list(1:10,1:10)
Error in
On Mon, Feb 27, 2012 at 3:18 PM, ikuzar raz...@hotmail.fr wrote:
Hello,
I'd like to classify data with kmeans algorithm. In my case, I should get 2
clusters in output. Here is my data
colCandInd colCandMed
1 82 2950.5
2 83 1831.5
3
On Fri, Feb 24, 2012 at 3:47 PM, Adel ESSAFI adeless...@gmail.com wrote:
Hello,
I want to create 10 dataframe using a for loop.
I don t know what to do to create 10 different dataframes whose name is
parametrized with variable i.
This syntaxe fails. It create a unique fataframe called dfn.
On Tue, Feb 21, 2012 at 1:44 PM, array chip arrayprof...@yahoo.com wrote:
Hi, I have a microarray dataset from Agilent chips. The data were really log
ratio between test samples and a universal reference RNA. Because of the
nature of log ratios, coefficient of variation (CV) doesn't really
Good advice. But perhaps ?mad or some other perhaps robust plain old
measure of spread?
The problem is not (lack of) robustness to outliers, the problem is to
find genes whose expression variation is small compared to (mean)
expression. Trouble is, Agilent throws the mean expression
On Wed, Feb 15, 2012 at 10:22 PM, arunkumar akpbond...@gmail.com wrote:
Hi,
My input is
x=c(D,A,B)
Y=c(A,B,C,D)
varorder=which(Y %in% X)
I'm getting result as 1 2 4
But i need the result to be 4 1 2
Here's a hint: lookup the function match.
Peter
On Thu, Feb 9, 2012 at 1:46 AM, Gregory Jefferis jeffe...@gmail.com wrote:
Dear Peter,
Trying to respond to your original question
Thanks for staying on thread :)
I have a git repositiory in the root of my packages:
ie
package-foo/.git
package-foo/R
package-foo/inst
Running make
Hi all, in particular package developers,
I'm exploring using a version control system to keep better track of
changes to the packages I maintain. I'm leaning towards git (although
mercurial also looks good) but am not sure what is the best way to set
up the repository. It seems I can't set the
You need to use set.seed() or one of the random number generators to
have .Random.seed defined. Also, if you load a previously saved
workspace and that workspace had a .Random.seed defined, you will have
it defined.
HTH
Peter
On Tue, Feb 7, 2012 at 9:58 AM, Wilkerson, Sylvia (NIH/CIT) [E]
Well, if you look at your data more carefully, you will see that the
histogram of y is heavily skewed towards 1 (small values). The 91/625
quantile is still 1 (there are 192 1s). It is therefore not surprising
that RF comes up with mostly 1s (in my attempt it came up with two 2s,
but that is a bit
Not sure why you think the formula does not hold... but am guessing
you think that sin(x) and cos(x) are have values in [-1, 1]? Well that
only holds for real x. If you have a complex x, sin(x) and cos(x) are
unbounded - indeed, if you can write x=iy and y is real, you can show
(up to my own
On Mon, Jan 30, 2012 at 11:43 AM, Joseph Park josephp...@ieee.org wrote:
Thanks Michael Peter.
Michael's expansion makes sense.
This is what I expected:
a = pi + 0i
complex( real = cos(Re(a)), imaginary = sin(Im(a)) )
[1] -1+0i
As they say, the error is between the keyboard and the
ehm... this doesn't take very many ideas.
x = runif(n=10e6, min=0, max=1000)
x = round(x)
system.time( {
y = x[-1] - x[-length(x)]
})
I get about 0.5 seconds on my old laptop.
HTH
Peter
On Fri, Jan 27, 2012 at 4:15 PM, Kevin Ummel kevinum...@gmail.com wrote:
Hi everyone,
Speed is the
On Fri, Jan 20, 2012 at 9:04 AM, Martin Batholdy
batho...@googlemail.com wrote:
Hi,
I am currently trying to z-transform (that is subtracting the mean and divide
by the standard deviation) multiple columns of a data.frame at the same time.
My first approach was:
x - data.frame(c(0:10),
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