similar to: Calculating correlation for a big matrix

Dear All, I am trying to install R 2.7 on my openSUSE 10.3. I have faithfully followed instruction at http://cran.r-project.org/bin/linux/suse/ReadMe.txt. I have downloaded all the RPMs but still R complains about: libtcl8.4.so is needed by R-base-2.7.1-6.1.i586 I searched for this library and found a one, tcl-8.4.15-22.i586.rpm at openSUSE distribution site and installed. But R still complains

Dear All, It is not a typical R question (though I use R for this) but I thought someone will help me. For the list of P values, I have calculated FDR using p.adjust() in R (bioconductor). But my FDR values are same for all the P values. When do we get same FDR values? Does the smallest P values should less than 1/N? (where N is the number of P values) Thanks in advance. Kind regards, Ezhil

Dear All, I have large matrix (46000 x 11250). I would like to do the linear regression for each row. I wrote a simple function that has lm() and used apply(mat,1,func). The issue is that it takes ages to load the file and also to finish the lm. I am using LINUX 64 bit with 32G mem. Is there an elegant and fast way of completing this task? Thanks in advance. Kind regards, Ezhil

Dear All, I have two matrices A (40 x 732) and B (40 x 1230) and would like to calculate correlation between them.  I can use: cor(A,B, method="pearson") to calculate correlation between all possible pairs. But the issue is that there is one-many specific mappings between A and B and I just need to calculate correlations for those pairs (not all). Some variables in A (proteins, say p1)

Dear All, I am using the following commands to do the scatter plot of two vectors, say X and Y. plot(X,Y, col="blue") abline(a=1,b=1, col="red") abline(a=-1,b=1, col="green") I would like to split the scatter plot into 3 part with 3 different colors: (i) points lies between 2 lines, (ii) points above line 1, and (iii) points below line 2. I am struggling to do

Dear All, How can I store hist() or any plot output graphics in PNG format? I tried with bitmap() but not getting the result. Appreciate your help on fixing this. Thanks in Advance. Regrads, Ezhil

Dear All, I have a correlation matrix of size 100 x 100 and would like to extract the diagonal matrix from it. I have used the for loop to store tha correlation values of the diagonal matrix. Is there a 'R way' of doing this? Thanks in advance. Kind regards, Ezhil

Dear All, I have matrix (50000 X 60) of subjects and their responses to a set of questions. All responses are classified into categories (500). I would like to average all subject's responses for each category. I wrote a code using a for loop but is not working. Could please tell me what's wrong with the code? I guess, there is a elegant R way of doing the same thing. Thanks in advance.

Dear all, I am having a data for 2 different treatments with different time points. So, I used the following code to plot the boxplot and also to do anova. T11 <- c(280, 336, 249, 277, 429) T12 <- c(400, 397, 285, 407, 313) T13 <- c(725, 373, 364, 706, 249) T21 <- c(589, 257, 466, 248, 913) T22 <- c(519, 424, 512, 298, 907) T23 <- c(529, 479, 634, 354, 1015) obs <- c(T11,

Hi, I have a matrix HR(9x27). I would like to make a single vector with elements: t(HR[,1]) followed by t(HR[,2]) and then t(HR[,3] ... etc. Is there any neat way of converting this matrix into a vector rather doing something like c(t(HR[,1]), t(HR[,2]), t(HR[,3]) ..)? Thanks in Advance. Kind regards, Ezhil ____________________________________________________________________________________

Dimitris Rizopoulos wrote: > look at ?rowMeans; you can also use "apply(mat, 1, mean)" but > rowMeans() is better. By my reading of the question, this is not what Ezhil wants. He said: ``I have a 992 x 74 matrix. I would like to form a new matrix by averaging each 4 rows from the original one.'' I.e. he wants (I think) the first row of the new matrix to be the

Hi guys I have an input file with multiple columns and and rows. Is it possible to calculate correlation of certain value of certain No (For example x of S1 = 112) with all other values (for example start with x 112 corr a 3 of S1 = x-a 0.2 ) INPUT ******* No S1 S2 S3 S4 Sn a 3 4 45 34 23 x 112 0 12 23 0 b 0 1 23 12 1 n 0 1 0 1 1

Dear all ?Hmisc::rcorr states that it takes as main argument "a numeric matrix". But is it normal that it fails in such an ugly way on a data frame? (See below.) If the function didn't attempt any conversion to a matrix, I would have expected it to state that in the error message that it didn't accept 'data.frame' objects in its input. Also, I vaguely remember having used

Hey Everyone, Im fresh new in R, and Im supposed to write a code to give me a correlation between two rankings. So I have two ranking lists, which contain file names, e.g.: Ranking list 1: file1.java file3.java file2.java Ranking list 2: fiile2.java file4.java file1.java I need to see how much are these two ranking lists are alike, get a correlation between them. I dont even know where to

Dear all I'd like to make a beeping sound in R, but alarm() doesn't beep? I checked ?alarm but I couldn't find any pointers to system configuration. Any ideas? Regards Liviu > sessionInfo() R version 2.14.2 (2012-02-29) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5]

Dear all, I installed the amd64 cran2deb [1] JGR binaries on a fresh Debian testing, and JGR is missbehaving. When JGR starts up, one core of the CPU goes to 100% and stays there, even though I am keeping it idle and not performing any operation. I tried JGR with both sun-java6-jdk and openjdk-6-jdk, debian-liv:/home/liviu# update-alternatives --config java There are 4 choices for the alternative

Dear all, Given the following vector: > (z <- c('R project', 'hello world', 'something Else')) [1] "R project" "hello world" "something Else" I know how to obtain all capitals or all lower case letters: > tolower(z) [1] "r project" "hello world" "something else" > toupper(z) [1] "R

Dear all This may be obvious, but I cannot get it working. I'm trying to subset & sort a data frame in one go. x <- iris x$Species1 <- as.character(x$Species) ##subsetting alone works fine with(x, x[Sepal.Length==6.7,]) ##sorting alone works fine with(x, x[order(Sepal.Length, rev(sort(Species1))),]) ##gets subsetted, but not sorted as expected with(x, x[(Sepal.Length==6.7) &

Dear R users I would like to do some spreadsheet style expansion of dates. For example, I would need to obtain a vector of months. I approached in an obviously wrong way: > paste(01:12) [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" > as.Date(paste(01:12),

Hi all, Could you please help me? I am having the following weird problem when debugging R programs using "browser()": In my function, I've inserted a "browser()" in front of Step 1. My function has 3 steps and at the end of each step, it will print out the message "Step i is done"... However, after I hit <ENTER> when the program stopped before Step 1