similar to: Multiple color schemes for barchart (lattice)

Hi, I am a new user of "R", I am trying to read my data in.. "Cervixhc.dat" used to be in a different directory, now it has been moved to "O:\E&s\APC cervix FINAL (YG,MC,MD)\Manuscript\Data", but when I ran the following program (in red) I got an error message "Error in setwd(dir) : cannot change working directory", and "Error in file(file,

Hi all, Suppose I have a vector like this: [1] "STAT1" "STAT1" "STAT1" "STAT1" "GAPDH" "GAPDH" "GAPDH" "ACTB" "ACTB" [10] "ACTB" "DDR1" "RFC2" "HSPA6" "PAX8" "GUCA1A" "UBE1L" "THRA" "PTPN21" [19]

Hi, I have the following function: > kurtosis <-function(x) (mean((x-mean(x))^4))/(sd(x)^4) #x is a vector and data > print(mydata) V1 V2 V3 V4 V5 1 1007_s_at DDR1 2865.1 2901.3 1978.3 2 1053_at RFC2 103.6 81.6 108.0 3

Hi, i have two files (file1.txt and file2.txt) which i would like to merge, based on certain criteria, i.e. it combines data based on matching geneID and exons. i have used the merge option, but it does not give me the desired outcome. merged.txt shows the result i would like. *File1. txt* ** AffyProbe ProbeType Flag GeneSymbol GeneID Exons Chrom Strand Affytart AffyEnd 1

Dear R-helpers I have a problem related to the use of NLME I think is simply a matter of getting the nlme coding correct, but i cannot get my brain around it I am analysing some 24 growth curves of some cells , and i wanted to say that there are significant differences between the curves in two parameters that describe the pattern of growth. these parameters are from a logistic (r & k)

I need to generate venn diagrams for some of my data. I am using the venn library. Is there a function that generates the ids and attributes that I can pass on to venn Library(venn) ids <- c(1,1,1,2,2,2,3,3,3,4,4,5,5,5,6,6,7,8,9,10) attributes <-

Hello R-help group, I have a question about merging lists. I have two lists: Genes list (hSgenes) name chr strand start end transStart transEnd symbol description feature ENSG00000223972 1 1 11874 14412 11874 14412 DEAD/H box polypeptide 11 like 1DEAD/H box polypeptide 11 like 3DEAD/H box polypeptide 11 like 9 ;;

Hi: I have made a lot of progress reading and manipulating large data files, thanks to the help of several of you. I am now stuck with writing the final file with the following error (see also the full transcript below): Error in as.matrix.data.frame(x) : length of dimnames[2] not equal to array extent I do not know what it means and could not find how to get around that in the manual nor

We are trying to read a sas export file into R. (Works fine on Mac by ftping the export file from solaris box and then importing to R with read.xport, this gives rational numbers etc.) Trying to do this on an IBM Power p655 running linux, reading the same sas export file as used on MAC, in this case the results are not rational. Many of the numbers are interpreted as INF etc. Is it possible

Hi list, I have a question about using *read.table()* to read in a txt file. Basically, it consists of 16346 rows, 6 columns (no header). The code I used is: exprSet <- read.table('process_all4_GSA2.txt', row.names = 1,header =FALSE) and I got an error message: > exprSet <- read.table('process_all4_GSA2.txt', row.names = 1,header =FALSE) Error in

Hi, i have two files (file1.txt and file2.txt) which i would like to merge, based on certain criteria, i.e. it combines data based on matching geneID and exons. i have used the merge option, but it does not give me the desired outcome. merged.txt shows the result i would like. *File1. txt* ** AffyProbe ProbeType Flag GeneSymbol GeneID Exons Chrom Strand Affytart AffyEnd 1

Hi, I was wondering if I might be able to ask some advice about doing residual plots for the lmer function in the lme4 package. Our group's aim is to find if the expression staining of a particular gene in a sample (or "core") is related to the pathology of the core. To do this, we used the lmer function to perform a logistic mixed model below. I apologise in advance

Hi useRs - I was wondering if anyone out there can tell me where to find R-code to do mixes of tables and graphics. I am thinking of something similar to this: http://yost.com/information-design/powerpoint-corrupts/ or like the excel routines people are demonstrating: http://infosthetics.com/archives/2006/08/excel_in_cell_graphing.html My aim is to provide small graphics to illustrate

I would like to organize my data as follows: I have a table that contains various data, and the numbers represent a level of similarity between these data, eg RF00013 has 100% similarity with the data RF00014. I would leave my table as a heatmap where darker colors represent higher similarity, and the lighter colors represent less level of similarity. I'm using version 2.11 of R. these

Dear Dr Hornik / R help list, I am using the mda package and in particular the fda routine to classify a set of 162 neurons falling in to 11 neuronal cell types according to 17 morphological variables. I would like to use a cross-validation approach in which I split the data, train with one part amd then test the predictive accuracy of the discriminant functions with the remaining part. However

My goal is simple: calcuate GC content of each sequence in a list of nucleotide sequences. I have figured out how to vectorize, but all my attempts at memoization failed. Can you show me how to properly memoize my function? There is a StackOverflow post on the subject of memoization, but it does not help me: http://stackoverflow.com/questions/7262485/options-for-caching-memoization-hashing-in-r

Here is an example of how to do it. > library(survival) > vfit <- coxph(Surv(time, status) ~ celltype + trt, data=veteran) > userinput <- data.frame(celltype="smallcell", trt = 1) > usercurve <- survfit(vfit, newdata=userinput) #the entire predicted survival curve > user2 <- summary(usercurve, time= 2*365.25) # 2 year time point > user2$surv [1]

Debuggers, I wrote to r-help about this and was appropriately told off by Peter Dalgaard. I append that mail in case you have not seen it. Following Peter's advice I have attempted to simplify the problem. First note that the following does *not* fail (by which I mean crash, as in generate a memory access violation): > tmp<-matrix(c(1,0,0,1,1,1),2,3) >

Dear users, In a study with recurrent events: My objective is to get estimates of survival (obtained through a Cox model) by rank of recurrence and by treatment group. With the following code (corresponding to a model with a global effect of the treatment=rx), I get no error and manage to obtain what I want : data<-(bladder)

It would be nice if the 00check.log file also included this part of the output: Running ?bladder.R? Comparing ?bladder.Rout? to ?bladder.Rout.save? ... OK Running ?book1.R? Comparing ?book1.Rout? to ?book1.Rout.save? ... OK Running ?book2.R? Comparing ?book2.Rout? to ?book2.Rout.save? ... OK etc. The survival package has enough test scripts that it exceeds my terminal's scroll