similar to: substituting own test statistics in a built-in function

Dear everyone, I am trying to do a Wilcoxon one-sided test on my gene expression data. These are the data i have in R: data.matrix (matrix, numeric) containing all gene expression data (42 rows=genes, 42 columns=tumors), no column header or row names data.cl (vector, numeric) consisting of 42 0's and 1's to indicate class 0 or class 1 for each column in data.matrix I want to do a

Hi there, Does R has built-in codes for nonpara. bivariate regression so that I can estimate the joint distribution of two variables as a function of some covariates? Thanks a lot. --------------------------------------------------- Ximing Wu Department of Economics University of Guelph Guelph, Ontario, Canada, N1G 2W1 Tel: (519) 842-4120, ext 53014 Fax: (519) 763-8497 email: xiwu at

Hello R experts, I am trying to analyze this dataset and am stuck on this problem for quite some time now. I am using mt.rawp2adjp. the output that came out was a matrix with two colums since I had asked it to calculate the adjusted p values using one method. so it has the two columns as: rawp BH I combined these using cbind with my actual dataframe. checked using head all was fine. thereafter I

The function knn.cv in the class package doesn't have error checking to ensure that the length of the classlabel argument is equal to the number of rows in the test set. If the classlabel is short, the result is often a segfault. > library(class) > dat <- matrix(rnorm(1000), nrow=10) > cl <- c(rep(1,5), rep(2,5)) > cl2 <- c(rep(1,5), rep(2,4)) > knn.cv(dat, cl) [1] 2

Add a new constant ETH_P_802_3_MIN, the minimum ethernet type for an 802.3 frame. Frames with a lower value in the ethernet type field are Ethernet II. Also update all the users of this value that David Miller and I could find to use the new constant. Also correct a bug in util.c. The comparison with ETH_P_802_3_MIN should be >= not >. As suggested by Jesse Gross. Compile tested only.

> dim(data.sub) [1] 10000 140 #####extracting all differentially express genes########## library(multtest) two_side<- (1-pt(abs(data.sub),50))*2 diff<- mt.rawp2adjp(two_side) all_differ<-diff[[1]][37211:10000,] all_differ #####list of differentially expressed genes########## > probe.names<- + all_differ[[2]][all_differ[[1]][,"BY"]<=0.01] Error in

Hi All I am new to R and I am not sure of how this should be done. I have a matrix of 985x100 values and the class is data.frame. A sample of my dataset looks like this (Since its a huge dataset and it would make the screen look more complex, I am pasting only the first few rows and columns. V2 V3 V4 V5 V6 2 0.009953966 -0.01586103 -0.016227028

Hi All I have a symmetric matrix of genes ( 100x100 matrix). I also have a matrix (100x2) of two columns where column 1 has the gene names and column 2 has the cluster it belongs to (they are sorted and grouped based on the cluster no). I would like to order the rows and columns of the 100x 100 matrix such that the first n genes correspond to cluster 1 and next n genes correspond to cluster 2

Hi, I am using SAM (from siggenes_1.2.11 package) method to select genes from a microarray data set. After installing the latest R2.4.0 on my computer, to my surprise the results are totally different from that calculated using R2.1.1. Even the example code doesn't work the same way under these two versions of R. Does anybody know what is going on? Thanks for any suggestions.

Hi All I would like to know how to access the values of the variable lambda.mu and and see what abs(lambdas[1]) does since lambdas is not a keyword. Snippet of the code: scoreFunction <- function(lambdas) { lambda.mu <- abs(lambdas[1]) sme.em(yi,tmei,Xi,Ni,G,lambda.mu,lambda.v)$AICc } Thanks in advance. Regards Ap -- Aparna Sampath Master of Science (Bioinformatics)

I had build ocfs2-tools-1.2.3 from sources on x86_64 machine (FC6). When I run: ocfs2console I get: Traceback (most recent call last): File "/usr/local/sbin/ocfs2console", line 3, in ? from ocfs2interface.about import process_args ImportError: No module named ocfs2interface.about When I try: locate ocfs2interface.about I get no result. Any ideas what went wrong ? Regards, Andy

Hi all, My data genes [,1] [,2] [,3] [,4] [1,] 25 72 23 55 [2,] 34 53 41 33 [3,] 26 43 26 44 [4,] 36 64 64 22 [5,] 47 72 67 34 stu<-t.test(genes[,1:2],genes[,3:4]) > stu$p.value [1] 0.4198002 i get 1 pvalue for the entire col1:col2 Vs col3:col4. I am trying to get 5 p values for the 5 rows i have. I am trying to avoid a for loop coz my

Dear helpers I want to use rpart several times in a loop to build a classification tree. My problem is that rpart needs a formula as argument and for that the variables need to have names and this doesn't happen in my case. Every iteration in the loop has a different dataset with several variables (ex. 38 or more) and so I can't type the names by hand every time. Is there any function

Is there any function in R like is.not.found(x, y) meaning if you can't find object x, then use object y?? Mikkel Grum

Hi I have a data frame with 40,000 rows and 4 columns, one of which is "class". For each row, the "class" column can be one of 10 possible NUMERIC values. I wish to substitute these numeric values with words/characters. For example, I wish to substitute all occurences of "5467" in the column "class" with "alpha", "7867" with

Hello all, I have a Samba configured as a member server to Winnt domain. Its using ADS authentication. All was well - but now when I type smbstatus I get the error msg: INFO: Current debug levels: all: True/5 tdb: False/0 printdrivers: False/0 lanman: False/0 smb: False/0 rpc_parse: False/0 rpc_srv: False/0 rpc_cli: False/0 passdb: False/0 sam: False/0 auth: False/0

Hello! Assuming I have a vector, such as v <- c(1,2,1,2,3,3,1) This vector has three unique elements: 1, 2, and 3. > unique(v) [1] 1 2 3 If I shuffle this vector of unique elements, I get something like this: > sample(unique(v)) [1] 3 2 1 In the vector v I started with, I would now like to replace each element in unique(v) with the corresponding element (i.e. the element with the

Hi everybody, In Splus, the following works fine. foo1 <- function(x, const) x + const foo2 <- function(x, const) x * const const1 <- 1 const2 <- 2 foo <- substitute(function(x) { a <- foo1(x, const1) b <- foo2(a, const2) b }, list(const1=const1, const2=const2)) foo(1:3) In R, the code doesn't work, as foo is of mode "call", and

I have a simple (!) problem. What I want to do is to create a legend with Greek letters, and substituting numbers into the legend. Like this: mu=1:3 Mean=rep(mu, each=20) plot(runif(60), rnorm(60,Mean,0.1), pch=Mean) # create a plot legend(0.6,1.7, paste("mu =", 1:3), pch=mu) but with a Greek letter mu. I think the solution has something to do with substitute() possibly along with

I am running R version 2.8.1 on Windows XP OS. I generate and write a .csv file from my R script. Then the following command works to upload it to a remote server using a windows batch file that carries out the ftp (among other things). > system("C:/upload_data/uploadq8.bat C:/upload_data/out_2009-02-26.csv", wait=FALSE) I want to set this up to run daily and create a unique