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Hi, I am trying to run affylmGUI on my mac computer. I have already installed the Tlc package as well as Bwidgets through ActiveTcl conversion installing files. However, when running affylmGUI() on R, I keep getting the message in the attached file. I have copied the tcl folders from the root library to the user library, and have obtained the same issue. I would really appreciate if

Hello, I would like to reshape my data for presentation purposes from something like this: > test <- data.frame(a=c("A","A","A","A","B","B","B"),b=c(1,1,2,2,1,1,1),c=1:7) > test a b c 1 A 1 1 2 A 1 2 3 A 2 3 4 A 2 4 5 B 1 5 6 B 1 6 7 B 1 7 to something like this: a b c 1 A 1 1,2 3 A 2 3,4 5 B 1 5,6,7 This seems

Hi, I am trying to produce a plot with an xlabel that reads (x >= 5%) with the >= turned into the correct epression. I can do this up to the percentage sign by specifiing xlab=expression(x>=5). Whatever I do to include the % sign as well doesn't seem to work. xlab=bquote(x>=5.("%")) almost works but includes brackets. Anyonw know how to solve this one Dan PS I am

Hello, I would like to scrape some html tables from a web page and convert them to a data.frame so I can perform further analysis. Could anyone tell me the best way to do this? Would it be more appropriate to use an external tool first? Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis

Hello, I have a data.frame like this: a 1,2,3,4 b1 b 6,7 b3 And I would like to transform it to this: a 1 b1 a 2 b1 a 3 b1 a 4 b1 b 6 b3 b 7 b3 I have been looking at ddply but can't seem to work it out. ANy help would be gratefully received. Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis

Hello, I would like to be able to calculate the age of someone at a particular date. Both dates are date objects. Here is what I have come up with: floor(as.numeric(sampleInfo$Date.of.DIAGNOSIS-sampleInfo$Date.of.birth)/365.25) Is this the best approach? or is there an inbuilt function? I have looked at difftime but that does not seem to allow output in years. Many thanks Dan --

Hello, I have a data.frame which I would like to sort with the primary key decreasing while the secondry key is increasing e.g. x <- data.frame(One=c(1,1,1,2,2,3,4,5),Two=c(2,3,1,2,3,3,3,3)) I would like to order it so it looks like this: One Two 8 5 3 7 4 3 6 3 3 4 2 2 5 2 3 3 1 1 1 1 2 2 1 3 i.e. primarily decreasing in the 1st column but if there is a

Hello, I have a gene expression matrix with columns being samples and rows being genes. I would like to display the expression values for each gene. I have two groups which I colour differently. The aim is to see if there is any difference between the two groups consistently across genes. So the following works well:

Hello, I am getting a GPG error with the ubuntu repository at the bristol UK mirror. When my source.list has this line: deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu/ intrepid/ On an "apt-get update" you get this: W: GPG error: http://www.stats.bris.ac.uk intrepid/ Release: The following signatures were invalid: BADSIG D67FC6EAE2A11821 Vincent Goulet <vincent.goulet at

Hello, I would like to calculate the 95% confidence intervals for the estimates of a linear model and I just wanted to check that I am doing it correct. Is it just: Estimate + 1.95996*Std.Error to Estimate - 1.95996*Std.Error or is there another approach that doesn't assume a normal distrbution? Thanks. Apologies for my naiivity Dan --

Hello, I am finding that the melt function from the reshape library causes errors when applied to a data.frame that contains numeric and character columns. For example, melt(id.vars="ID",data.frame(ID=1:3,date=c("a","b","c"),value=c(1,4,5))) ID variable value 1 1 date a 2 2 date b 3 3 date c 4 1 value <NA> 5 2

Dear all, For a population of about 200 I have a continuous variable and an ordinal variable. The question I would like to ask is whether the continuously increases (or decreases) as the rank of the ordinal variable increases. I was thinking that a Spearmen's rank correlation or or a chi squared trend might be appropriate. I don't have any experience dealing with ordinal variables so I

Hi, I have a script that takes a subset of genes on a microarray and tries to fit a coxph model to the expression values for each gene. This seems to work fine but in some cases it produces warnings and/or errors. For example: Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: In fitter(X, Y,

Hi, I have a particular barplot I would like to generate, but I am having trouble getting it to work. What I would like is in effect two barplots with stacked bars merged into one. For example, I have two samples (yoda1,yoda2) on which I measure whether two variables (var1,var2) are present or absent for a number of measurements on that sample. > var1 <- data.frame(yoda1=c(3,7),

Does anyone have any ideas how I could do a power calculation for a log rank test. I would like to know what the suggested sample sizes would be to pick a difference when the control to active are in a ratio of 80% to 20%. Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Email: daniel.brewer at icr.ac.uk

Hello, I might be barking up the wrong tree here, but I want to make sure I have a full understanding of this. What I would like to know is what tests are performed to give the p-values for each variable in the table that is the result of coxph regression when the variables are categorical only. More specifically, when expected counts are less than 5 is the Fisher's exact test used instead

Hello, I would like to test some data to see whether it has the shape of a step function (i.e. y1 up until x_th and then y2 where x_th is the threshold). The threshold x_th is unknown and the x values can only take discrete values (0,1,2,3,4). An example would be: data<- data.frame(x=1:20,y=c(rnorm(10),rnorm(10,10))) I was thinking along the lines of fitting some sort of piiecewise linear

I would like to do some power estimations for a log-rank two sample test and cpower seems to fit the bill. I am getting confused though by the man page and what the arguments actually mean. I am also not sure whether cpower takes into account censoring or not. Could anyone provide a simple example of how I would get the power for a set control/non-control clinical trial where censoring occurs at

Hi, Is there anyway to set up R so that it uses a SOCKS proxy in Linux? I am getting some strange issues with the Institute's new web filtering system and want to be able to test whether a problem I have with the biomaRt package is caused by it. Many thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular

Hi, I am trying to do a power calculation for a difference in proportions test where I want to estimate the sample size required. I know (well estimate) that group one (n1) is 10% of the population and group 2 (n2) is 90% of the population. I know the effect size (h). pwr.2p2n.test only allows one variable to be left null whereas I would like both n1 and n2 to be determined where I know there