I will be out of the office starting 09/11/2007 and will not return until
12/11/2007.
You may contact Fong Chee Weng (DID: 63259191 or [EMAIL PROTECTED])
should you require any urgent information assistance. Else I will return
your email when back.
Have a great day!
Hwee Pin
_
Hi,
I would like to know if there is an algorithm in R for testing if a data set as
a normal destribution.
Thank you for your time,
Pedro Marques
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the
?ks.test
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of [EMAIL PROTECTED]
Sent: Friday, November 09, 2007 4:46 AM
To: r-help@r-project.org
Subject: [R] Testing Normal Distributions
Hi,
I would like to know if there is an algorithm in R for testing if
There is a whole package to do this: nortest
David Scott
On Thu, 8 Nov 2007, [EMAIL PROTECTED] wrote:
>
>
> Hi,
>
> I would like to know if there is an algorithm in R for testing if a data set
> as a normal destribution.
>
> Thank you for your time,
>
> Pedro Marques
>
> _
Luca Penasa wrote:
> Hi everybody,
> Im a newbie, but i hope someone can help me in this work...
> Ill try to explain what i need to do in the best way, but my english is
> not good...
> Iv imported a big table of data, this table is something like this:
>
> 255 0 255 0 255 255 255 0 255 0
> 255
Hi
I am a newbie to R but have tried a number of ways in R to do this and
can't find a good solution. (I could do it out of R in perl or awk but
would like to know how to do this in R).
I have a large data frame 49 variables and 7000 observations however for
simplicity I can express it in the f
Hi
[R-2.6.0, macOSX 10.4.10].
The helppage says that rowSums() and colSums()
are equivalent to 'apply' with 'FUN = sum'.
But I came across this:
> a <- matrix(1:30,5,6)
> is.integer(apply(a,1,sum))
[1] TRUE
> is.integer(rowSums(a))
[1] FALSE
>
so rowSums() returns a float.
Why is this?
Hello All,
Sorry everybody for another message on this topic but I don't understand the
times off execution that I have.
From my search in the forum I found that linux old be better to this kind of
operation, so now I using a dualCore 2.33GHz with 8Gb RAM but the times off
execution don´t decreas
Hi
I would like to try out JGR but can't install and run it. I run vista
and that shouldn't be a problem since JGR supports vista since 1.5.1.
When running the installer with the --debug flag in an admin shell it
download the packages and the following error message comes up.
"One or more packag
Sandy Small wrote:
> Hi
> I am a newbie to R but have tried a number of ways in R to do this and
> can't find a good solution. (I could do it out of R in perl or awk but
> would like to know how to do this in R).
>
> I have a large data frame 49 variables and 7000 observations however for
> simp
Dear Bill Venables,
Does this mean that in a conventional aov object, the "summary.lm" gives
the parameter estimates and p-values computed "marginally", while the
"summary.aov" table by default gives sequential sums of squares?
This question arose recently when a colleague and I were discussing
?shapiro.test
On 08/11/2007, [EMAIL PROTECTED] <[EMAIL PROTECTED]>
wrote:
>
>
>
> Hi,
>
> I would like to know if there is an algorithm in R for testing if a data
> set as a normal destribution.
>
> Thank you for your time,
>
> Pedro Marques
>
> __
> R-h
This is not about slowness of Linux nor of R but of a particular function
in a contributed package. Few of us are familiar with that package, and
you have not given a reproducible example. Please do as the posting guide
asked and talk directly to the maintainer (who may well not read this
lis
Also see the tests in the energy package for univariate and multivariate
normality (normal.etest and mvnorm.etest).
The test for univariate normality has very similar properties as the
Anderson-Darling test.
Maria Rizzo
Dept. of Mathematics & Statistics
Bowling Green State University
At 06:57
Thanks for reply, Moshe.
let's assume that the latent class model is the simplest one, 1 Y with
gaussian distribution, 1 X, and 2 latent classes (A and B). Of course
we can't assume that all my cases are from one class. Otherwise, why
do I need to use latent class model?
for each latent class, we h
Thanks for your suggestion Marc. I saw that on some Oracle-related
web-sites, but something in the way RODBC functions verify the existance of
a table does not accept that naming structure. For example:
> sqlColumns(eids, "EIDS.TEST_ARTCL_INST")
Error in sqlColumns(eids, "EIDS.TEST_ARTCL_INST") :
Dear all,
probably this is quite clear for most of you but for me it is a headache...
I am regressing response A against the continuous covariate B and the
relationship is clearly quadratic.
When I add a second covariate B, the relationship becomes linear for both B and
C.
So, I expect that
Hello,
EXAMPLE
##Create time series
bb_500 = scan("my_file.dat")
ts <- ts(bb_500, frequency=168)
ts
Time Series:
Start = c(1, 1)
End = c(3, 164)
Frequency = 168
[1] 61 60 60 59 58 58 58 58 58 61 64 65 65 64 64 64 63 63 62 61 60 60 60
59 58
[26] 58 58 57 57 57 57 56 57 57 58 59 59 59 60 60
On Nov 9, 2007 5:56 AM, Sandy Small <[EMAIL PROTECTED]> wrote:
> Hi
> I am a newbie to R but have tried a number of ways in R to do this and
> can't find a good solution. (I could do it out of R in perl or awk but
> would like to know how to do this in R).
>
> I have a large data frame 49 variables
Yea, this is exactly what I wanted! I really appreciate your help.
Thanks,
Gang
On Nov 8, 2007, at 7:46 PM, jim holtman wrote:
> I think something like this is what you are after. This will create 7
> pairs of lists with the parameters that I think you want. I don't
> have the data (if you wa
I just installed R 2.6.0 (had R 2.5 before).
Here is my problem. Usually, when I work with R I first go to
"File->Change dir" and browse to a folder that seats OUTSIDE of the
folder "C:\Program Files\R\R-2.6.0" and then create my script there
(and open and re-open it there). I never had any problem
On Fri, 9 Nov 2007, Mark Lyman wrote:
> Thanks for your suggestion Marc. I saw that on some Oracle-related
> web-sites, but something in the way RODBC functions verify the existance of
> a table does not accept that naming structure. For example:
>
>> sqlColumns(eids, "EIDS.TEST_ARTCL_INST")
> Err
Thank you very much.
That works nicely.
The trick I particularly needed was "within"which I didn't know about.
Also nice to get a data frame out with "sparseby" instead of just a
mulit-array with "by"
Sandy
Duncan Murdoch wrote:
> Sandy Small wrote:
>> Hi
>> I am a newbie to R but have tried a nu
This is not the address of the package maintainer (nor of the person
who wrote to you), nor is that a reproducible example (we don't have
my_file.dat). Please DO study the posting guide!
On Fri, 9 Nov 2007, Joao Santos wrote:
Hello,
EXAMPLE
##Create time series
bb_500 = scan("my_file.dat")
Dimitri Liakhovitski gmail.com> writes:
>
> I just installed R 2.6.0 (had R 2.5 before).
> Here is my problem. Usually, when I work with R I first go to
> "File->Change dir" and browse to a folder that seats OUTSIDE of the
> folder "C:\Program Files\R\R-2.6.0" and then create my script there
> (
Have you tried using 'setwd'? I have no problem with changing
directories and executing scripts. Can you provide an example of the
script that you are trying to execute? How does it "crash"? Does is
to it only when you 'source' it? More information is needed.
On Nov 9, 2007 10:21 AM, Dimitri
On 11/9/2007 10:22 AM, Sandy Small wrote:
> Thank you very much.
> That works nicely.
> The trick I particularly needed was "within"which I didn't know about.
within() is new in 2.6.0; it's a nice addition. There's also
transform() which could be used in this situation, replacing
within(subset,
I don't try to execute any script. I am just trying to create a
completely new (empty) script file and save it OR open any existing
script file (that might even be empty).
My actions are (and by the way - I work under Windows XP professional
- and I worked with it before - with R 2.5):
1. Change di
What OS is this? (Yes, I can guess it is Windows, but there seems to be a
bug in changing working directory under Vista that got exposed in R
2.6.0.)
What does 'crash' mean (the posting guide did specifically ask you not to
use that word)?
This is of course not how the rw-FAQ suggests you mak
Dear All,
A quick question: I need to generate a lot of graphs via an R script.
To speed up things, I typically define automatically a ylim parameter
ranging from the minimum to the maximum of the represented data.
However, some of the graphs are not easy to read since the lower /
higher tick on th
Hello again,
I read the posting guide and now I could send the example.
I also send a mail directly to Prof. Rob J Hyndman that is the maintainer of
package forecast and if I have a answer I will send it to the list.
ts <-
structure(c(61, 60, 60, 59, 58, 58, 58, 58, 58, 61, 64, 65, 65,
64, 64,
Here is another approach using transform and ave which I think is a
little simpler than the others suggested:
> new.data <- transform( iris,
+ normSW = Sepal.Width / ave(Sepal.Width, Species, FUN=max),
+ normSL = Sepal.Length / ave(Sepal.Length, Species, FUN=max)
+ )
You can adjust it for y
I'm not able to install R 2.6.0 on my Mac running 10.5. When running
the installer, and after agreeing to the license, in the "Installation
Type" stage, the Packages are all greyed out (R framework and R GUI
for MAC OS X), and therefore the "Install" button in the lower right
is greyed out
Hi, I have an efficiency question.
To centralise a dataset (in a data frame) I have been using:
a <- mean(Data)
Data <- t(t(Data)-a)
...to force row-wise recycling.
Is there a better/more efficient/more elegant way than transposing the dataset
twice?
Thanks
[[alternative HTML version
Hi everyone, I would like to write VBA macros for accessing R and it is my
first attempt. I really could use some help here.
I am trying to use the following code to read data from Access. The R code
between "" is correct as I successfully run it from R, but when I call it
using VBA, it comes out
?scale or ?sweep or ?lapply
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Mark Deacon
> Sent: Friday, November 09, 2007 6:47 AM
Dear R-help -
Thanks to those who replied yesterday (Christos H. and Thomas L.)
regarding my question on coxph and model formula, the answers worked
perfectly.
My new question involves the following.
I want to run several coxph models (package survival) with the same
dataset, but different su
Hi all,
I would also be very interested in a solution to that (although I know that
using orthogonal contrasts
is usually the method of choice)
All the best
Christoph
Andrew Dolman schrieb:
> Dear list members,
>
> Can anyone please point to an example of how to use glht(multcomp) with lmer
>
Dear John and the rest,
Finally, it seems that now I have found a solution for the problem:
options(width=200) #make window size bigger
#create a test dataset (which is a correlation matrix)
#with row and col names
#extract from this matrix only those correlations
#that fulfill a specific criter
Hi folks - After upgrading to the latest version of Rmetrics, I can't
read in data like I used to. Is anyone seeing the following? It seems
to truncate the dates after I use "as.timeSeries".
-John
SP500<-read.table("SP500.csv",header=TRUE,sep=",")
> head(SP500)
DateOpenHig
The following variation of what you proposed will allow you to either subset
the dataset outside coxph or to use the subset argument:
subwrap5 <- function(x, sb=NULL) {
coxph(Surv(times,event)~trt, data = x, subset = sb)
}
subwrap5(testdf, testdf$sex == 'F')
subwrap5(testdf[testdf$sex == 'F',
I want to compute confidence intervals for the random effect estimates
for each subject. From checking on postings, this is what I cobbled
together using Orthodont data.frame as an example. There was some
discussion of how to properly access lmer slots and bVar, but I'm not
sure I understood. Is th
In terms of recommended approach, I think it would be easier to generate
subsetting conditions as (lists of) logical vectors and use those as
suggested before. It seems to me more cumbersome to use the data to
generate logical conditions as text strings and then parse those within your
wrapper to
I have recently installed R v. 2.6.0. I am running Windows XP. I have done the
package update as recommended by Brian Ripley.
I wish to create a PDF version of a graph but I am getting the error messages:
Error: Invalid font type
In addition: Warning messages:
1: font family not found in PostS
what has been suggested, for a while on the mailing list now, is to
upgrade R to the patched version.
On Nov 9, 2007, at 12:47 PM, Kris Lockyear wrote:
>
> I have recently installed R v. 2.6.0. I am running Windows XP. I have
> done the package update as recommended by Brian Ripley.
>
> I wish
Sorry about the post, but the FAQ weren't helping me. I recently
installed R (2.6.0) for windows on my laptop which runs Vista
ultimate. I can do all the functions in R except saving. Whenever I
try to save I get an error saying "unable to find .Rhistory" Any
ideas would be appreciated.
-C
Hi,
Works for me, try this:
SP500$Date <- as.character(as.Date(as.character(SP500$Date), "%m/%d/%y"))
SP500
DateOpenHigh Low Close Volume
1 2006-08-04 1280.26 1292.92 1273.82 1279.40 2530970112
2 2006-08-03 1278.22 1283.96 1271.25 1280.27 2728440064
3 2006-08-02 1270.73
On Fri, 2007-11-09 at 10:01 -0800, Bert Gunter wrote:
> Ummm...
>
> Define: "Confidence interval for BLUP" .
>
> I know what a confidence interval for a parameter or function of parameters
> (which is what a predicted value is) is; but a BLUP is neither, so I don't
> get what a confidence interva
Ummm...
Define: "Confidence interval for BLUP" .
I know what a confidence interval for a parameter or function of parameters
(which is what a predicted value is) is; but a BLUP is neither, so I don't
get what a confidence interval for it should mean.
Feel free to reply off list, as this is clear
Hi, I am performing a paired wilcox.test (ie wilcoxon signed ranked test) on
two samples for testing if they are similar.
1. I would like to test whether they are similar not at point 0 difference
rather than on a more flexible, ie if they differ by more than 5 units let's
say. Is this possible to
Greg Snow wrote:
> Here is another approach using transform and ave which I think is a
> little simpler than the others suggested:
>
>
>> new.data <- transform( iris,
>>
> + normSW = Sepal.Width / ave(Sepal.Width, Species, FUN=max),
> + normSL = Sepal.Length / ave(Sepal.Length, Species
Hi,
I want to analyse a contigency table (3 x 12) with a fisher.test
beacause there are cells that are less than 5.
Ämmen Anken Baf Belchen Höchi Hof Porti Räm Schmutz Schön Sissa Tann
class14 726 150 246 68 126 66 331 7 61
class24 7 6 55
On Fri, 9 Nov 2007, Kris Lockyear wrote:
>
> I have recently installed R v. 2.6.0. I am running Windows XP. I have done
> the package update as recommended by Brian Ripley.
>
> I wish to create a PDF version of a graph but I am getting the error messages:
>
> Error: Invalid font type
> In additi
On Fri, 9 Nov 2007, Rick Bilonick wrote:
> On Fri, 2007-11-09 at 10:01 -0800, Bert Gunter wrote:
>> Ummm...
>>
>> Define: "Confidence interval for BLUP" .
>>
>> I know what a confidence interval for a parameter or function of parameters
>> (which is what a predicted value is) is; but a BLUP is nei
On Fri, 9 Nov 2007, Denis Aydin wrote:
> Hi,
>
> I want to analyse a contigency table (3 x 12) with a fisher.test
> beacause there are cells that are less than 5.
...expected cells. Anyways, your data set yields a statistic > 160
and I wouldn't worry that this could be the result of random variat
On Fri, 9 Nov 2007, Prof Brian Ripley wrote:
> This is of course not how the rw-FAQ suggests you make use of R, and
the
> best recommendation is to follow the FAQ's workflow.
The workflow recommendation that I read in the FAQ is:
2.5 How do I run it?
Just double-click on the shortcut you prep
On Fri, 2007-11-09 at 18:55 +, Prof Brian Ripley wrote:
> I think Bert's point is important: I picked up a student on it in a case
> study presentation on this week because I could think of three
> interpretations, none strictly confidence intervals. I think 'tolerance
> interval' is fairl
Hi,
I have a query regarding usage of hist (histogram) function in R.
I have a data where the range of the x -axis is from 0.0-1.0. When I use
hist the ticks on the x-axis it gives me by default is at
0.0,0.2,0.4,0.6,0.8 and 1.0.
If I want more ticks such that the x-axis has 0.0,0.1,0.2,
see also ?cut
Justin BEM
BP 1917 Yaoundé
Tél (237) 99597295
(237) 22040246
- Message d'origine
De : "[EMAIL PROTECTED]" <[EMAIL PROTECTED]>
à : sigalit mangut-leiba <[EMAIL PROTECTED]>
Cc : r-help <[EMAIL PROTECTED]>
Envoyé le : Vendredi, 2 Novembre 2007, 22h33mn 52s
Objet : Re: [
Perhaps you can do:
x <- runif(50, 0,1)
hist(x, axes=F)
axis(2)
axis(1, at=seq(0,1, by=0.1), labels=seq(0,1, by=0.1))
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O
On 09/11/2007, Manisha Brahmachary <[EMAIL PROTECTED]> wrote:
>
> Hi,
>
>
>
> I have a query regard
X is a matrix and F is a vector.
F2 <- data.frame(cbind(X,F))
F2
V1 V2V3 F
1 -0.250536332 -1.4755883 1.9580974 -2.136487
2 -0.009856084 0.4953269 0.5486092 -2.744482
3 -0.406962682 0.7729631 0.1861905 -2.891821
4 1.938780097 0.7469251 1.2537781 -1.212992
5 -0.332
Hi,
Thanks for your prompt reply. I tried out the code and it works. Currently
my code is something like this:
hist(all$PI_HAT, labels=T, main="PI_HAT distribution (All)",
xlab="PI_HAT",ylab="count", col="gray",ylim=c(0,15))
May I ask you, what does runif(50,0,1) mean? How do I intergr
I am having the same problem upgrading R 2.6.0 on leopard (Mac OS
10.5) as well. Any insight would be appreciated.
Lanre
On Nov 9, 2007 10:54 AM, Jason Horn <[EMAIL PROTECTED]> wrote:
> I'm not able to install R 2.6.0 on my Mac running 10.5. When running
> the installer, and after agreeing to th
Try this:
hist(all$PI_HAT, labels=T, main="PI_HAT distribution (All)",
xlab="PI_HAT",ylab="count", col="gray",ylim=c(0,15), axes=F)
axis(2)
axis(1, at=seq(0,1, by=0.1), labels=seq(0,1, by=0.1))
runif generate a sample of Uniform Distribution, see ?runif.
--
Henrique Dallazuanna
Curitiba-Paraná-
Hi,
I have been having trouble finding references that compare the classical
decomposition methods [function decompose()] with the STL method of
Cleveland et al. (1990) [function stl()]. The decompose() help page refers
to the method as a much more sophisticated decomposition but I am looking
fo
Please see and search the R-sig-mac mailing list.
-Don
At 3:04 PM -0500 11/9/07, Lanre Okusanya wrote:
>I am having the same problem upgrading R 2.6.0 on leopard (Mac OS
>10.5) as well. Any insight would be appreciated.
>
>Lanre
>
>On Nov 9, 2007 10:54 AM, Jason Horn <[EMAIL PROTECTED]> wrote:
>>
Hello,
Currently I am using R for building a logistic model using numerical and
nominal data as predictors. Before doing the regression, the predictors are
grouped. The groups I determine manually by trying to maximize the information
value (which is an indicator for the discriminatory power o
Hi all,
It seems that I can get White's (HC3) test using MASS. The syntax I
used for the particular problem is
anova(scireg3, white.adjust="hc3")
where scireg3 is an object from the lm function. But, the anova summary
table is all I get. I don't get the new estimates or standard errors
co
Hi is there a package for diagonal linear discriminant
analysis (diagonal LDA)?
Thanks
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and pro
supclust
On 11/9/07, array chip <[EMAIL PROTECTED]> wrote:
> Hi is there a package for diagonal linear discriminant
> analysis (diagonal LDA)?
>
> Thanks
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE d
I am attempting to run Poole's OC package in R, using Windows NT 5.1.
Everytime I try to estimate a two-dimensional model, the estimation begins
and then I am informed "R for Windows GUI front-end has encountered a
problem and needs to close". There is no problem estimating a
one-dimensional mod
SASxport Version 1.2.2 is now available
---
The SASxport package provides R with full support for reading
and writing SAS xport format files.
Version 1.2.2 corrects problems on 64 bit versions of R.
SASxport 1.2.2 is available _now_ at
http://random-
Dear All,
Can R perform multivariate integration with infinite limits of integration?
Thanks in advance,
Paul
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/p
Hi:
I need to plot two data sets and then I need to change labels of xaxis. I
can manage to achieve something like it with this:
x<-data.frame(a=c(1,2,3,4,5),b=c(2,4,6,8,10))
y<-data.frame(a=c(3,4,5),b=c(1.5,2,2.5))
xts <- ts(x$b,start=x$a[1])
yts <- ts(y$b,start=y$a[1])
ts.plot(xts,yts,col=c("re
Try this:
ts.plot(xts,yts,col=c("red","blue"), gpars = list(axes = FALSE))
axis(2)
axis(1, 2:10/2, letters[2:10])
On Nov 9, 2007 7:54 PM, Felipe <[EMAIL PROTECTED]> wrote:
> Hi:
>
> I need to plot two data sets and then I need to change labels of xaxis. I
> can manage to achieve something like it
Dear List,
Hi! I am wondering what is the simplest way to subset a portion of columns
from a matrix.
For example, there is a matrix A (238,304*243). What is the simplest
way to get a sub-matrix B which comprises of column 1, 3, 5, 7,9,...(odd column
number) from matrix A?
Thank you very much for
There are many ways. For example, you can do something like
A[seq(1,dim(A)[2],2)]
Julian
Julian M. Burgos
Fisheries Acoustics Research Lab
School of Aquatic and Fishery Science
University of Washington
1122 NE Boat Street
Seattle, WA 98105
Phone: 206-221-6864
affy snp wrote:
> Dear List
Hi Julian,
Thanks for the help!
Best,
Allen
On Nov 9, 2007 11:08 PM, Julian Burgos <[EMAIL PROTECTED]> wrote:
> There are many ways. For example, you can do something like
>
> A[seq(1,dim(A)[2],2)]
>
> Julian
>
> Julian M. Burgos
>
> Fisheries Acoustics Research Lab
> School of Aquatic a
No problem. Actually, I missed a comma. You should do
A[,seq(1,dim(A)[2],2)]
Julian
affy snp wrote:
> Hi Julian,
>
> Thanks for the help!
>
> Best,
> Allen
>
>
>
> On Nov 9, 2007 11:08 PM, Julian Burgos <[EMAIL PROTECTED]> wrote:
>
>> There are many ways. For example, you can do some
I figured that out. I appreciate!
Allen
On Nov 9, 2007 11:25 PM, Julian Burgos <[EMAIL PROTECTED]> wrote:
> No problem. Actually, I missed a comma. You should do
>
> A[,seq(1,dim(A)[2],2)]
>
> Julian
>
>
>
> affy snp wrote:
> > Hi Julian,
> >
> > Thanks for the help!
> >
> > Best,
> > All
Or perhaps:
A[, seq(1, ncol(A), 2)]
On Nov 9, 2007 11:25 PM, Julian Burgos <[EMAIL PROTECTED]> wrote:
> No problem. Actually, I missed a comma. You should do
>
> A[,seq(1,dim(A)[2],2)]
>
> Julian
>
>
>
> affy snp wrote:
> > Hi Julian,
> >
> > Thanks for the help!
> >
> > Best,
> > Allen
>
Dear list,
I need to read in a big table with 487 columns and 238,305 rows (row names
and column names are supplied). Is there a code to read in the table in
a fast way? I tried the read.table() but it seems that it takes forever :(
Thanks a lot!
Best,
Allen
Thanks!
Allen
On Nov 9, 2007 11:34 PM, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> Or perhaps:
>
> A[, seq(1, ncol(A), 2)]
>
>
> On Nov 9, 2007 11:25 PM, Julian Burgos <[EMAIL PROTECTED]> wrote:
> > No problem. Actually, I missed a comma. You should do
> >
> > A[,seq(1,dim(A)[2],2)]
> >
> >
If they are all numeric, you can use 'scan' to read them in. With
that amount of data, you will need almost 1GB to contain the single
object. If you want to do any processing, you will probably need a
machine with at least 3-4GB of physical memory, preferrably a 64-bit
version of R. What type of
1. You might be able to speed it up somewhat by specifying
colClasses=.
2. Another possibility is that the devel version of
the sqldf package provides an interface which simplifies reading a data file
into sqlite and from there into R. This is particularly useful if you
don't want to read it all
Hi Jim,
Thanks a lot! I am currently running it on my laptop but without any
success. I could upload it to a server which is with 8Gb memory
and it might be better to go from there.
Actually, I could have the whole file splitted in two parts,
one with 2nd column to 95th column, the other one with
If they are all numeric, then read it in with:
x <- scan('yourfile', what=0) # assuming blank separators
This will create a single vector of the values. Now this comes in in
row order if that is what your data file has, so you could just add
dimensions of
dim(x) <- c(487, 238305)
rows and col
Here is an example of reading in file of 3M numbers (11MB of text
file) on my laptop:
> system.time(x <- scan('/tempyy', what=0))
Read 300 items
user system elapsed
6.220.166.53
> str(x)
num [1:300] 1 2 3 4 5 6 7 8 9 10 ...
> gc()
used (Mb) gc trigger (Mb) max use
Thanks Jim.
I tried:
A<-read.table(file="243_47mel_withnormal_expression_log2.txt",
+header=TRUE,row.names=1,colClasses=c('factor', rep('numeric',486)))
by specifying colClass but it did not work.
The error message I got is:
> A<-read.table(file="243_47mel_withnormal_expression_log2.txt",heade
Hi Gabor,
Thanks a lot!
The header of the big file looks like as follows:
probe_set
WM_806_Signal_A
WM_806_call
WM_1716_Signal_A
WM_1716_call
I only need those columns with the header as like _Signal_A
Can you suggest how to use sqldf?
Thanks!
Allen
On Nov 9, 2007 11:47 PM, Gabor Groth
Your data is mixed: numeric and characters/factors. You can use
skip=1 to skip the header line, but it looks like the rest is mixed.
In you example there are only 5 columns; are you just showing the
first 5 columns? if there is the pattern that you show, then you
would have a scan like:
scan('yo
On Nov 10, 2007 12:19 AM, affy snp <[EMAIL PROTECTED]> wrote:
> Thanks Jim.
>
> I tried:
>
> A<-read.table(file="243_47mel_withnormal_expression_log2.txt",
> +header=TRUE,row.names=1,colClasses=c('factor', rep('numeric',486)))
>
> by specifying colClass but it did not work.
>
> The error message I
Hi Jim,
Actually besides the first column which is character, half of the 486 columns
are character as well.
Thanks!
Allen
On Nov 10, 2007 12:29 AM, affy snp <[EMAIL PROTECTED]> wrote:
> Hi Jim,
>
> I tired scan() first and got
>
> > x <- scan(file="243_47mel_withnormal_expression_log2.txt", wh
Hi Jim,
I tired scan() first and got
> x <- scan(file="243_47mel_withnormal_expression_log2.txt", what=0)
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
scan() expected 'a real', got 'probe_set'
So I guess it requires the file be numeric. But I do have row names
It sounds like the data is not all numeric; you have a 'factor' in
your read statement. It also sounds like either some of your lines
are incomplete in the number of columns since are you trying to read
in a "B" as a numeric. So if you have a character, then one way of
doing it is:
x <- scan('yo
Yes, I am showing the first 5 columns as an example. Thank you very much
for your suggestion. Let me check it out.
Allen
On Nov 10, 2007 12:39 AM, jim holtman <[EMAIL PROTECTED]> wrote:
> Your data is mixed: numeric and characters/factors. You can use
> skip=1 to skip the header line, but it loo
BTW, sth like:
A<-read.table(file="243_47mel_withnormal_expression_log2.txt",
+header=TRUE,row.names=1,colClasses=c('factor', rep('factor',486)))
will do anything good?
Allen
On Nov 10, 2007 12:41 AM, affy snp <[EMAIL PROTECTED]> wrote:
> Yes, I am showing the first 5 columns as an example. Tha
If you want to read only the alternate columns that contain numerics,
then you can probably use:
scan('yourfile', what=c(rep(list(NULL), list(0)), 243), flush=TRUE,
fill=TRUE, skip=1)
On Nov 10, 2007 12:25 AM, affy snp <[EMAIL PROTECTED]> wrote:
> Hi Gabor,
>
> Thanks a lot!
>
> The header of the
On Nov 10, 2007 12:25 AM, affy snp <[EMAIL PROTECTED]> wrote:
> Hi Gabor,
>
> Thanks a lot!
>
> The header of the big file looks like as follows:
>
> probe_set
> WM_806_Signal_A
> WM_806_call
> WM_1716_Signal_A
> WM_1716_call
>
>
> I only need those columns with the header as like _Signal_A
>
Thanks Gabor.
I made the column names look like as:
probeset
WM806SignalA
WM806call
WM1716SignalA
WM1716call
And I then tried what you mentioned and got:
> library(sqldf)
Loading required package: gsubfn
Loading required package: proto
> source("http://sqldf.googlecode.com/svn/trunk/R/sql
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