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...that it needs to use the http_proxy environment variable. And I apologise for being blunt, but that is an R problem, not a proxy problem! Thanks for your help Mick -----Original Message----- From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] Sent: 24 July 2003 16:56 To: michael watson (IAH-C) Subject: RE: [R] Your proxy seems not to work with R (was R won't connect to the internet on Linux!) When I do (under tcsh) env http_proxy=http://wwwcache.bbsrc.ac.uk:8080/ R > options(internet.info=0) > update.packages() trying URL `http://cran.r-project.org/src/contrib/PACKAGES...

Quite a simple one really! When I run boxplot(), the labels on the X axis are horizontal, and I want them vertical. So I did: par(las=3) boxplot(...) And my labels just aren't there anymore.... Any help???

Hi When I use plot(hclust(dist..)...)...) etc to create a dendrogram of a hierarchial cluster analysis, I end up with a vertical tree. What do I need to do to get a horizontal tree? Also, my users are used to seeing trees who's leaves all "end" at the same place (eg. Like in minitab). Is this possible in R? Thanks Mick Michael Watson Head of Informatics Institute for Animal

Hi I did a google search on this and came up with nothing. OK, in the latest release of R for windows, I want to change the gui to SDI mode. Edit -> GUI preferences Choose SDI Apply I get the message about properties not being able to be changed on a running console, and that I need to save. So I click Save, and am met with a "Save As" dialogue box with the default file called

Hi Forgive my ignorance. I am selecting a column of a data.frame using the column name, and I want to know what the resulting column "is". My data frame is called "submin" and the column name is held in a variable called "display.gname" Eg: > is.data.frame(submin) [1] TRUE > is.data.frame(submin[,display.gname]) [1] FALSE >

Hi When I give the command: > heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="row ",trace="none",col=greenred.colors(79)) The resulting heatmap has re-ordered my columns! This is time-course data, and I don't want my columns re-ordered! Note from the help: Rowv: determines if and how the _row_ dendrogram should be reordered.

Hi Sorry to ask such a basic question. I have a list, each element of which is a vector of two values. What I actually want is a matrix with two columns, and one row per element of the list. Obviously I have tried as.matrix(), and as.vector() but I didn't expect the latter to work. I feel so lame asking this. Any suggestions? Mick

OK, I really am struggling with this one! Forgive me if I am being stupid.... I am running R 1.7.1 on Suse Linux 8.1. I connect to the internet through a proxy so I have: IAHC-LINUX03:~ # echo $http_proxy wwwcache.bbsrc.ac.uk:8080 IAHC-LINUX03:~ # echo $HTTP_PROXY wwwcache.bbsrc.ac.uk:8080 just in case ;-) SO, i go into R and I get: > source("http://www.bioconductor.org/getBioC.R") unable to connect to 'www.bioconductor.org' on port 80. Error in...

Hi I have data from 12 subjects. The measurement is log(expression) of a particular gene and can be assumed to be normally distributed. The 12 subjects are divided into the following groups: Infected, Vaccinated, Lesions - 3 measurements Infected, Vaccintaed, No Lesions - 2 measurements Infected, Not Vaccinated, Lesions - 4 measurements Uninfected, Not Vaccinated, No Lesions - 3 measurements

OK, dumb question, and it is probably in the docs somewhere, but after 12 months working with R and quite a while looking at the docs, I still don't know (or have forgotten) how to replace all NA values in a matrix at once with some other value. I can do it column by column using is.na(), but I can't figure out how to do it for the whole matrix. My apologies, I am ashamed ;-) Michael

I think that title makes sense... I hope it does... I have a data frame, one of the columns of which is a factor. I want the rows of data that correspond to the level in that factor which occurs the most times. I can get a list by doing: by(data,data$pattern,subset) And go through each element of the list counting the rows, to find the maximum.... BUT I can't help thinking there's

Hi I have seen a few posts to this list regarding problems accessing the x11() device over cgi - namely, when trying to create a graphic using the jpeg() function, everything is fine from the command line but it won't work over cgi, producing the error: "Unable to open connection to X11 display" Has anyone actually solved this particular problem satisfactorily? Please reply

Hi This is a difference between the way matrices and data frames work I guess. I want to replace the NA values in a data frame by 0, and the code works as long as the data frame in question actually includes an NA value. If it doesn't, there is an error: df <- data.frame(c1=c(1,1,1),c2=c(2,2,NA)) df[is.na(df)] <- 0 df df <- data.frame(c1=c(1,1,1),c2=c(2,2,2)) df[is.na(df)] <-

Hi I have a complicated plot which has a potentially large legend. What I want to do is actually create the legend in a new window. Has anyone done this before? I'd like to be able to create a window with just the legend in it, and have it so the window is just the right size etc. I'm sure someone must have done this already? If not, any tips would be welcome. Thanks Mick

Hi I am performing an analysis of variance with two factors, each with two levels. I have differing numbers of observations in each of the four combinations, but all four combinations *are* present (2 of the factor combinations have 3 observations, 1 has 4 and 1 has 5) I have used both anova(aov(...)) and anova(lm(...)) in R and it gave the same result - as expected. I then plugged this into

Hi I've been reading the help for by and aggregate but can't get my head round how to do this. I have a data frame - the first three columns are replicate measurements, then the next 3 are replicates etc up to 36 (so 12 variables with 3 replicate measurements each). I want to compute the mean for each of the 12 variables, so that, for each row, I have 12 means. A grouping variable

Hi We have touched on this before, but I don't think I quite got it right. So I have a list, each element of which is a a vector of 2 numbers: > l2 $cat000_a01 [1] 0.3429944 4.5138244 $cat000_a02 [1] 0.1929336 4.3064944 $cat000_a03 [1] -0.2607796 4.1551591 What I actually want to convert this into is a matrix with the names (cat000_a01 etc) as row names, the first element of each of

Hi Is there a function for computing the standard correlation coefficient (not pearson) in R? Thanks Mick

...eed to use the greek CAPITAL letter delta in the mtext() function. I got as far as expression(delta) but this gives me the lowercase version. Can anyone help? I'm using R 2.7 on Windows XP Mick Head of Informatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 http://www.iah.ac.uk/research/bioinformatics/bioinf.shtml The information contained in this message may be confide...{{dropped:14}}

Hi I have been creating very, very long jpeg images for the last two weeks using jpeg(). All of a sudden, and I mean that, it's stopped working - I've not changed a thing! The error message I get is: > jpeg("out.jpg",width=50000,height=480, quality=100) Error in devga(paste("jpeg:", quality, ":", filename, sep = ""), width, : unable