[R] Finding matches in 2 files

I have 2 files containing data analysed by 2 different methods. I would like to find out which genes appear in both analyses. Can someone show me how to do this? _ [[trailing spam removed]] [[alternative HTML version delet

Re: [R] ROC curve in R

http://search.r-project.org/cgi-bin/namazu.cgi?query=ROC&max=20&result=normal&sort=score&idxname=Rhelp02a&idxname=functions&idxname=docs there is a lot of help try help.search("ROC curve") gave Help files with alias or concept or title matching 'ROC curve' using fuzzy matching: granulo(ade4)

[R] ROC curve in R

Hi, I need to build ROC curve in R, can you please provide data steps / code or guide me through it. Thanks and Regards Rithesh M Mohan [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/

[R] colored heights in 3D plot (persp)

Hello everybody, I have a matrix with measurement values and plot them with persp. I want to highlight different heights in different colors. At least everything above and under a certain z-level shall have a different color to make the differences in height more obvious. How can I do that or do

Re: [R] question on using "gl1ce" from "lasso2" package

G'day Li, On Wed, 25 Jul 2007 00:50:43 -0400 "Li Li" <[EMAIL PROTECTED]> wrote: > I tried several settings by using the "family=gaussian" > in "gl1ce", but none of them works. [...] > > gl1ce(Petal.Width~Sepal.Length+Sepal.Width+Petal.Length, > > data=iris,family=gaussian()) > Error in eval(expr,

[R] How to auto-scale cex of y-axis labels in lattice dotplot?

When I create a dotplot in lattice, I frequently observe overplotting of the labels along the vertical axis. On my screen, this illustrates overplotting of the letters: windows() reps=6 dat=data.frame(let=rep(letters,each=reps), grp=rep(1:reps, 26), y=runif(26*reps)) dotplot(let~y|grp, dat) Is

Re: [R] using contrasts on matrix regressions (using gmodels, perhaps)

The doBy package has an esticon function which allows you to do that. Regards Søren Fra: [EMAIL PROTECTED] på vegne af Ranjan Maitra Sendt: to 26-07-2007 01:30 Til: R-help Emne: [R] using contrasts on matrix regressions (using gmodels, perhaps) Hi, I want to

[R] using contrasts on matrix regressions (using gmodels, perhaps)

Hi, I want to test for a contrast from a regression where I am regressing the columns of a matrix. In short, the following. X <- matrix(rnorm(50),10,5) Y <- matrix(rnorm(50),10,5) lm(Y~X) Call: lm(formula = Y ~ X) Coefficients: [,1] [,2] [,3] [,4] [,5] (Inter

Re: [R] Subscript out of bounds when using datadist() from Design library

Chuck, Quite right. Thank you. Regards, -Cody -Original Message- From: Chuck Cleland [mailto:[EMAIL PROTECTED] Sent: Wednesday, July 25, 2007 4:33 PM To: Cody Hamilton Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Subscript out of bounds when using datadist() from Design library Cody

Re: [R] Subscript out of bounds when using datadist() from Design library

Cody Hamilton wrote: > I am running R version 2.4.1 on Windows XP. I have a question regarding the > datadist() function from the Design library. I have a data.frame (call it > my.data) with 4 columns. When I submit the code > > datadist(data=my.data) > > I get the following error message: >

Re: [R] Subscript out of bounds when using datadist() from Design library

Cody Hamilton wrote: > I am running R version 2.4.1 on Windows XP. I have a question regarding the > datadist() function from the Design library. I have a data.frame (call it > my.data) with 4 columns. When I submit the code > > datadist(data=my.data) You can just use dd <- datadist(my.data)

[R] Subscript out of bounds when using datadist() from Design library

I am running R version 2.4.1 on Windows XP. I have a question regarding the datadist() function from the Design library. I have a data.frame (call it my.data) with 4 columns. When I submit the code datadist(data=my.data) I get the following error message: Error in X[[1]] : subscript out of

Re: [R] [BioC] Color Question about image function in graphics package

Hello Shiliang, please have a look a the manual page for image (access from R by typing "?image" ). You can specify which colors to use and at which values to switch colors using the arguments breaks and colors. For example: image(matrix(rnorm(36),4,9)+20,col=c("red","blue"),breaks=c(-1e5,20,1e

[R] For loops

Hi, is there a way of simplifying the following code: G <- rep(NA,n) for(i in 1:n) { gj <- 0 for(j in 1:n) { for(l in 1:n) { for(m in 1:n) { gj <- gj+G.fun(XB[i]+p[3]*X[j,3]+p[4]*X[l,4]+p[5]*X[m,5],ff) } } } G[i] <- gj/n^3 } Thanks. Joaquim Santos _

[R] initalizing and checking validity of S4 classes

Dear Martin and Seth, Thanks a million for explanations and suggestions. I find myself still in the process of learning S4 system. Can you possibly suggest some material that I could use in this "process"? Anything apart from "Programming with data" book? I also know the notes written by John Cha

Re: [R] Updating packages in Ubuntu feisty for 2.5

On Wed, Jul 25, 2007 at 09:57:18PM +0200, Christophe Bonenfant wrote: > Hi - I do have exactly the same problem with the same distribution > (Ubuntu Feisty amd64) and am unable to upgrade to R 2.5.1. The > r-base-core is version 2.4.1 in Ubuntu depositories while all others > r-cran related pac

Re: [R] Updating packages in Ubuntu feisty for 2.5

Hi - I do have exactly the same problem with the same distribution (Ubuntu Feisty amd64) and am unable to upgrade to R 2.5.1. The r-base-core is version 2.4.1 in Ubuntu depositories while all others r-cran related packages are upgraded to R 2.5.1 (r-base-dev, r-base...). So far I have been uns

[R] Color Question about image function in graphics package

Dear Lists: I had a matrix which has lrt score for my microarray data. I just wonder how to visualize them with score over 20 in particular color such as blue. I cannot understand the color relationship with the value in z matrix. For example, If I see a red color in my image generated by image f

Re: [R] reversing the x-axis terms on a boxplot

Dylan Beaudette said the following on 7/25/2007 11:18 AM: > Hi, > > I am able to reverse the order of plotting on regular plots (i.e. with the > plot() function) by manually setting the xlim variable. > > Is there some trick like this which will work for a boxplot? > > * for example: > > l

Re: [R] if - else

try: Start <- ifelse (DateFirstEven < DateSecondEvent, (DateFirstEvent+DateSecondEvent)/2, DateFound) On 7/25/07, James J. Roper <[EMAIL PROTECTED]> wrote: > Greetings, > > I have some confusion with the use of if - else. Let's say I have a > four variables as follows: > > Condition

[R] Updating packages in Ubuntu feisty for 2.5

Hi, I would like to run R2.5.1 in Ubuntu feisty on an AMD64 chip. I am a total newbie to Linux. I have successfully compiled 2.5 however, I am not able to figure out how to upgrade the packages. I am not able to find an R-base-core_2.5.1-1_amd64 or all on the CRAN mirrors. I can find one on the Ubu

[R] DF and intercept term meaning for mixed (lme) models

Hi, I am using the lme package to fit mixed effects models to a set of data. I am having a difficult time understanding the *meaning* of the numDF (degrees of freedom in the numerator), denDF (DF in the denomenator), as well as the Intercept term in the output. For example: I have a groupedDa

[R] reversing the x-axis terms on a boxplot

Hi, I am able to reverse the order of plotting on regular plots (i.e. with the plot() function) by manually setting the xlim variable. Is there some trick like this which will work for a boxplot? * for example: l <- sample(letters, 500, replace=TRUE) n <- runif(500) boxplot(n ~ l) this will

Re: [R] initalizing and checking validity of S4 classes

Martin Morgan <[EMAIL PROTECTED]> writes: > Hi Michal -- > > Add validObject to your initialize method: Actually, a call to valid object is part of the default initialization method which has been masked. A different solution, which might have some other benefits is to delegate back to the defau

[R] if - else

Greetings, I have some confusion with the use of if - else. Let's say I have a four variables as follows: Condition DateFound DateFirstEvent DateSecondEvent NA10Jan2000 NA NA 0 05Jan2000

Re: [R] Constructing bar charts with standard error bars

John Zabroski gmail.com> writes: > > I am new to R. > > I want to graph group data using a "Traditional Bar Chart with Standard > Error Bar", like the kind shown here: > http://samiam.colorado.edu/~mcclella/ftep/twoGroups/twoGroupGraphs.html > > Is there a simple way to do this? [snip] >

Re: [R] Constructing bar charts with standard error bars

John Zabroski wrote: > I am new to R. > > I want to graph group data using a "Traditional Bar Chart with Standard > Error Bar", like the kind shown here: > http://samiam.colorado.edu/~mcclella/ftep/twoGroups/twoGroupGraphs.html There are severe problems with dynamite plots such as these. See ht

[R] qda(MASS) function error

Dear R user, I'm using qda (quadratic discriminant analysis) function (package MASS) to classify 58 explanatory variables (numeric type with different ranges) using a grouping variable (factor 2 levels "0" "1"). I'm using the qda method for class 'data.frame' (in this way I don't need to spec

Re: [R] Minitab Parametric Distribution Analysis in R

The survival package (survreg() function) will fit quite a few parametric models under censoring. If you aren't doing regression, but just one-sample fitting, you can feed the appropriate censored or truncated likelihood to mle() in the stat4 package. Both packages should be part of your R dis

Re: [R] Ggplot2 equivalent of axis and problem with log scale

On 7/25/07, ONKELINX, Thierry <[EMAIL PROTECTED]> wrote: > Dear useRs, > > Recently I've discorved ggplot2 and I must say that I really like it, > although the documentation still is a working in progress. > > My first question: How can I change the position of the labels and the > text of the labe

[R] Constructing bar charts with standard error bars

I am new to R. I want to graph group data using a "Traditional Bar Chart with Standard Error Bar", like the kind shown here: http://samiam.colorado.edu/~mcclella/ftep/twoGroups/twoGroupGraphs.html Is there a simple way to do this? So far, I have only figured out how to plot the bars using barplo

Re: [R] Odp: Open two graphic devices at a time

@Petr Hello, now I tried it with savePlot(). This is a very easy way. Now I don't need two devices. Thanks a lot MatzeK Petr Pikal wrote: > > Hi > > far from beeing an expert in graphic devices AFAIK you can either see your > graph on screen (x11 device) or to open other device (pdf, png,

[R] Odp: Open two graphic devices at a time

Hi far from beeing an expert in graphic devices AFAIK you can either see your graph on screen (x11 device) or to open other device (pdf, png, ...) and to issue plotting commands to that device. Do not forget dev.off() after your plot is finished. Or you can save your plot by menu command File

Re: [R] How to add circular text for a graph with concentric circles

Thanks, Jim. I tried to implement this but the text swings all over the place. I had thought that there could be a function where I could specify the circle's origin, radius and angle of the location of the starting letter, then, based on a specified font size and letter spacing, the arc could be p

[R] Time when object was created

Dear ComRades, Last night I left an Intel Core Duo Windows Vista system running an extensive mixed glm with lmer. This morning I found that R-lmer had finished the job successfully. I would like to know at what time the object containing the results (call it lme_1) was finished. I guess there i

[R] Open two graphic devices at a time

Hello, I would like to export my plots to harddisk (jpeg or pdf). I know that could be done with pdf(...) and jpeg(...). But my problem is that if I open e.g. the pdf device my plot does not appear on the screen. If I plot to the x11 device and try to export later the outputfile is damaged. How c

Re: [R] Rgraphviz and R 2.5.1 entry point Rf_allocString could not be located

On Wed, 25 Jul 2007, My Coyne wrote: > Dear R-Helpers > > In R 2.5.1, the command library(Rgraphviz) fails on my Windows (XP SP2) > system with error popup "The procedure entry point Rf_allocString could not > be located in the dynamic link library R.dll". > > Thanks in advance for any suggestion

Re: [R] Is Rwiki down?

Me too. Hank On Jul 25, 2007, at 7:50 AM, Jin Lo wrote: > Dear R-friends, > > is Rwiki down? I've been trying to login for the past > couple of days with no success. > > Yours sincerely, > > Jin > > > > > > __ > __ >

Re: [R] lme or gls prediction intervals

Hi Joris, Thank you for the reply. I also realize that I meant confidence intervals, not prediction intervals! I am trying to do something analogous to predict(model.gls, newdata, interval="confidence") but predict.gls does not have an interval argument. I am guessing that this is because it

[R] Rgraphviz and R 2.5.1 entry point Rf_allocString could not be located

Dear R-Helpers In R 2.5.1, the command library(Rgraphviz) fails on my Windows (XP SP2) system with error popup "The procedure entry point Rf_allocString could not be located in the dynamic link library R.dll". Thanks in advance for any suggestion in solving the error. My D. Coyne Imag

Re: [R] plots

--- amna khan <[EMAIL PROTECTED]> wrote: > Hi Sir > > I did not find any function of graph which plot one > variable on x-axis and 2 > or more than 2 variables on y-axis. I think ?points or ?lines may be what you want. > Moreover, how can I change the labels of L-moments > diagram obtained by

[R] Is Rwiki down?

Dear R-friends, is Rwiki down? I've been trying to login for the past couple of days with no success. Yours sincerely, Jin wherever you're surfing. __ R-

[R] Minitab Parametric Distribution Analysis in R

Minitab can perform a "Parametric Distribution Analysis - Arbitrary Censoring" with one of eight distributions (e.g., weibull), giving the maximum likelihood estimates of the parameters in the distribution for a given dataset. Does R have a package that provides equivalent functionality? Thanks for

[R] Odp: Operator > and

Hi you definitely shall make a quick glance to some documentation which comes with R e.g. R intro manual. Or look at CRAN where is quite impressive amount of literature from basic stuff to advanced papers. To your question: [EMAIL PROTECTED] napsal dne 25.07.2007 14:23:58: > > Hello, > > I

Re: [R] Operator > and

mm <- matrix(1:9, nrow=3) ; mm subset(mm[,1],mm[,1] <3) # Note I used 3 not 2 here. Have a look at some of the introductory documents on the R site ( Contributed documents under OTHER in the documentation). They should answer a lot of your basic questions like this. Documents by Lemon, Maindo

Re: [R] Operator > and

Yann Mauon wrote: > Hello, > > I'am new to the R world and have a lot of question but the first is : How to > deal with <> opertor in table objects? (Or how to deal with <> in > general...) I explain my problem. > > I read a file with the read.table expression. I then obtain a matrix. I read >

[R] Operator > and

Hello, I'am new to the R world and have a lot of question but the first is : How to deal with <> opertor in table objects? (Or how to deal with <> in general...) I explain my problem. I read a file with the read.table expression. I then obtain a matrix. I read the first line for example with t

Re: [R] problem with sub !

Try Sys.setlocale(). marco.R.help marco.R.help wrote: > > I am trying to use "sub" to replace patterns in a character array that > contains german names with german special characters. I have the following > problem: > >> sub("\\xdf","ss","Wei\xdferitzkreis") > Error in sub(pattern, repla

Re: [R] Obtaining summary of frequencies of value occurrences for a variable in a multivariate dataset.

Try summary: > summary(x) PR10 PR11 PR12 PR13 PR14 PR15 PR16 V:10 S:7 I:10 K:8 I:2 E:1 D:1 T:3 R:2 V:8 G:9 G:9 On 7/25/07, Allan Kamau <[EMAIL PROTECTED]> wrote: > A subset of the data looks as follows > > > df[1:10,14:20] > PR10 PR11 PR12 PR13 PR14

Re: [R] Obtaining summary of frequencies of value occurrences for a variable in a multivariate dataset.

Also if you want to access the individual values, you can just leave it as a list: > x.val <- apply(x, 2, table) > # access each value > x.val$PR14["V"] V 8 On 7/25/07, Allan Kamau <[EMAIL PROTECTED]> wrote: > A subset of the data looks as follows > > > df[1:10,14:20] > PR10 PR11 PR12 PR13 PR

Re: [R] Obtaining summary of frequencies of value occurrences for a variable in a multivariate dataset.

Is this what you want: > x <- read.table(textConnection(" PR10 PR11 PR12 PR13 PR14 PR15 PR16 + 1 VTIKVGD + 2 VSIKVGG + 3 VTIRVGG + 4 VSIKIGG + 5 VSIKVGG + 6

Re: [R] How to add circular text for a graph with concentric circles

[EMAIL PROTECTED] wrote: > Dear R experts, > > I am plotting the population of students who live in a city, and in > successive circular bands made of the contiguous districts that surround > the city. This is a stylized figure, where I specify the area of each > successive circle based on the

[R] Best-fit linear model for the two matrices plotted.

Hi all.. I am so far successful in plotting the matrices containing r-values and evol.distances using R. But I am facing a problem to fit a line to it. I tried using "lm" function but no success..!! Can you please help me for that? I am giving the functions, I tried, to get a plot here:

[R] Function polr and discrete ordinal scale

Dear all, To modelize the abundance of fish (4 classes) with a set of environmental variables, I used the polr and predict.polr functions. I would like to know how to bring the cumulated probabilities back to a discrete ordinal scale. For the moment I used the predict.polr function with the a

Re: [R] Strange warning in summary.lm

On Wed, 25 Jul 2007, ONKELINX, Thierry wrote: >> -Oorspronkelijk bericht- >> Van: Prof Brian Ripley [mailto:[EMAIL PROTECTED] >> Verzonden: woensdag 25 juli 2007 12:20 >> Aan: ONKELINX, Thierry >> CC: r-help@stat.math.ethz.ch >> Onderwerp: Re: [R] Strange warning in summary.lm >> >> On Wed

Re: [R] plotting gam models

What's wrong with the predict.gam(...,type="terms") suggestion (see yesterday)? Here's example code: ## example data from ?gam n<-400;sig<-2 x <- runif(n, 0, 1);z <- runif(n, 0, 1) x2 <- runif(n, 0, 1);x3 <- runif(n, 0, 1) f0 <- function(x) 2 * sin(pi * x) f1 <- function(x) exp(2 * x) f2 <- funct

[R] problem with sub !

Dear all, I am trying to use "sub" to replace patterns in a character array that contains german names with german special characters. I have the following problem: > sub("\\xdf","ss","Wei\xdferitzkreis") Error in sub(pattern, replacement, x, ignore.case, extended, fixed, useBytes) : inp

[R] Odp: plots

Hi [EMAIL PROTECTED] napsal dne 25.07.2007 12:17:54: > Hi Sir > > I did not find any function of graph which plot one variable on x-axis and 2 > or more than 2 variables on y-axis. ?matplot or you can do plot(x,y, ylim=range(all.your.y), type="n") and add lines/points by lines(x, one.of.yo

Re: [R] plots

amna khan wrote: > > I did not find any function of graph which plot one variable on x-axis and > 2 > or more than 2 variables on y-axis. > You can use xyplot() from the package lattice. library(lattice) xyplot(y1+y2+y3~x) I suspect, the problem is, that plot() erases everything that was plot

Re: [R] plotting gam models

Hi again, I have found a post in R.help archives made from someone who had the same problem when exporting the smooth function estimate got from a GAM, to plot it into another graphic software (http://finzi.psych.upenn.edu/R/Rhelp02a/archive/23136.html) However, I haven't found any reply to t

Re: [R] Obtaining summary of frequencies of value occurrences for a variable in a multivariate dataset.

A subset of the data looks as follows > df[1:10,14:20] PR10 PR11 PR12 PR13 PR14 PR15 PR16 1 VTIKVGD 2 VSIKVGG 3 VTIRVGG 4 VSIKIGG 5 VSIKVGG 6 VS

Re: [R] Strange warning in summary.lm

> -Oorspronkelijk bericht- > Van: Prof Brian Ripley [mailto:[EMAIL PROTECTED] > Verzonden: woensdag 25 juli 2007 12:20 > Aan: ONKELINX, Thierry > CC: r-help@stat.math.ethz.ch > Onderwerp: Re: [R] Strange warning in summary.lm > > On Wed, 25 Jul 2007, ONKELINX, Thierry wrote: > > > Dear P

Re: [R] Strange warning in summary.lm

On Wed, 25 Jul 2007, ONKELINX, Thierry wrote: > Dear Peter, Uwe and Brian, > > I've found some more problems with options(OutDec = ","). > > 1) as.numeric yields NA where it shouldn't It should: where does it say otherwise? OutDec affects output, only. > >> z <- c("12", "12,34", "12.34") >> opt

[R] plots

Hi Sir I did not find any function of graph which plot one variable on x-axis and 2 or more than 2 variables on y-axis. Moreover, how can I change the labels of L-moments diagram obtained by plotlmrdia(lmrdia()) Thank you -- AMINA SHAHZADI Department of Statistics GC University Lahore, Pakistan

[R] options(OutDec) etc {was "Strange warning in summary.lm"}

Without going into your details, I think options() should NEVER influence what as.numeric() does (which I think you are indirectly suggesting it should). In my eyes, using a decimal comma instead of decimal point in scientific computing is an abomination in itself. Providing an option for *out

[R] Ggplot2 equivalent of axis and problem with log scale

Dear useRs, Recently I've discorved ggplot2 and I must say that I really like it, although the documentation still is a working in progress. My first question: How can I change the position of the labels and the text of the labels? With a basic plot I would use axis(2, at = position.of.the.ticks,

[R] A problem with anova()

I fitted tree growth data with Chapman-Richards growth function using nls. summary(CR) Formula: HEIGHT ~ A * (1 - exp(-B * AGE))^C Parameters: Estimate Std. Error t value Pr(>|t|) A 29.007627 0.270485 107.24 <2e-16 *** B 0.030813 0.001095 28.13 <2e-16 *** C 1.849405 0.06865

Re: [R] Strange warning in summary.lm

Dear Peter, Uwe and Brian, I've found some more problems with options(OutDec = ","). 1) as.numeric yields NA where it shouldn't > z <- c("12", "12,34", "12.34") > options(OutDec = ",") > as.numeric(z) [1] 12,00NA 12,34 Warning message: NAs introduced by coercion in: as.double.default(z) #

Re: [R] Regarding Bivariate normal distribution.

Hi Arun i hope you will fin this document useful :) http://www.geocities.com/~mikemclaughlin/math_stat/Dists/Compendium.pdf no they cannot be found uniquely. as rightly pointed by Mr. Wolfgang, that there will be infinite pairs for each x you can get correspoinding y above document will be of

Re: [R] Regarding Bivariate normal distribution.

No, x and y are not unique. In fact, there is an infinite number of x and y pairs that are roots to the equation P[Xhttp://www.wvbauer.com/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Arun Kumar Saha Sent: Wednesday, July 25, 2007 08:58 To: r-help@

Re: [R] how to use "replace" for efficiency

You don't need to use 'replace', just use indexing in the assignment: isCrap <- apply((wheat2[,5:7] > wheat2[,8]), 1, any) wheat2[isCrap,5:7] <- NA Felix On 7/25/07, willem vervoort <[EMAIL PROTECTED]> wrote: > Hi > > I think I have been struggling to use replace correctly, I usually > work my w

[R] how to use "replace" for efficiency

Hi I think I have been struggling to use replace correctly, I usually work my way around this using a loop, but I think this is in fact inefficient. I have a dataset with runoff from three plots and associated rainfall. However either the datarecording was sloppy, or the rainfall very patchy. So

Re: [R] values from a linear model

On Tuesday 24 July 2007 12:02:58 Manuele Pesenti wrote: > Dear R users, > how can I extrapolate values listed in the summary of an lm model but not > directly available between object values such as the the standard errors of > the calculated parameters? thank you very much for all interesting ans

Re: [R] lme or gls prediction intervals

Martin, Have you checked ?intervals.gls This intervals are approximate, but this would be the obvious starting point to me. Joris "Martin Henry H.