similar to: DOE and interaction plot general question

[Apologies to Gabor, who I sent a personal copy of the reply erroneously instead of posting to List directly] [...] > Perhaps what you really intend is to > take the average over those elements in each row of the first matrix which correspond to 1's in the second in the corresponding > row of the second. In that case its just: > > rowSums(newtest * goldstandard) /

Hello R users, I am a fairly new R user, however, one of the problems I am having is the use of applying if-, and-, then-, else- statements in R against datasets & dataframe. Rtips mentions it, but without simple examples I am not quite sure what my syntax should look like. I am particularly interested in syntax that can be used with the transform function. for example if foo[,1] ==

I am trying to make a box plot and overlay it with a scatter plot from another data.frame. I was able to successfully create the boxplot, but when i tried using points(x~y...) the dots did not show up. example code aa<-(300,300,300,300,600,600,600,600,900,900,900,900) bb<-(13,12,14,11,56,44,34,75,22.,34,22,98,59,55,56) cc<-(13,12,14,11,56,44,34,75,22.,34,22,98,59,55,56)

Hello all, I am working with a 1000x1000 matrix, and I would like to return a 1000x1000 matrix that tells me which value in the matrix is greater than a theshold value (1 or 0 indicator). i have tried mat2<-as.matrix(as.numeric(mat1>0.25)) but that returns a 1:100000 matrix. I have also tried for loops, but they are grossly inefficient. THanks for all your help in advance. Lanre

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 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

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 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 --

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),

Hello, I have some data that has dates in the form 27.02.37. I convert them to a date object as follows: as.Date(data$date,format="%d.%m.%y") But this gives me years such as 2037 when I would like them to be 1937. I thought of trying to take off some time i.e. as.Date(camCD$DoB,format="%d.%m.%y") - 100*365 But that doesn't seem to work out correctly. Any ideas how to

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

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,

Hello, Is there a simple way to get the class type for each column of a data.frame? I am in the situation where I would like to get all the columns of a data.frame that are factors. I have tried: apply(df,2,class) but all the columns come back as class "character". Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of

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 --

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

I have a data.frame with rownames taken from a database. Unfortunately, one of the rownames (automatically obtained from the DB) is an empty string. I often do computations on the DB s.t. the answers (rows) are indexed with respect to the rownames so a computation on a DB record might necessitate the indexing into the data.frame by the emtpy row name. Unfortunately, that doesn't seem to

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