Re: [R] Correlation between 2 matrices but with subset of variables

, 2012 at 03:57:06PM > -0800, A Ezhil wrote: > > 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. B

[R] Issues in installing rgl in Mac OS 10.6.8

Dear All, I am trying to install rgl on my mac notebook from the source file. I tried using: /usr/bin/R64 CMD INSTALL rgl_0.92.798.tar.gz and get the following error message: checking for X... no configure: error: X11 not found but required, configure aborted. ERROR: configuration failed for pac

Re: [R] Correlation between 2 matrices but with subset of variables

Thanks a lot, Michael.  --- On Fri, 3/9/12, R. Michael Weylandt wrote: From: R. Michael Weylandt Subject: Re: [R] Correlation between 2 matrices but with subset of variables To: "A Ezhil" Cc: r-help@r-project.org Date: Friday, March 9, 2012, 7:59 AM Well, it would be possi

[R] Correlation between 2 matrices but with subset of variables

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

[R] Reordering the correlation matrix

Hi, I have a correlation matrix of 1000 x 1000 genes. I have grouped (20 groups) genes based on function and each gene has a index. I would like to reorder the correlation matrix based on the group index. Could you please suggest me how to do that? Thanks in advance. Kind regards, Ezhil

[R] Help with scatter plot

Dear All, I would like to add the mean line in the scatter plot by groups. I have plotted (X.val is 3 groups: 0, 1, 2): plot( Y ~ X.val). How can I add mean/median line (horizontal) for each group on the scatter plot? Thanks in advance. Kind regards, Ezhil

Re: [R] Working with large matrix

calculation fast? If you have any experience with large matrices, could you please share it with me? Thanks again, Ezhil --- On Fri, 9/11/09, Steve Lianoglou wrote: > From: Steve Lianoglou > Subject: Re: [R] Working with large matrix > To: "A Ezhil" > Cc: R-help@r-proj

[R] Working with large matrix

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

Re: [R] Averaging rows if a condition is true.

Thanks a lot, Mohamed. Kind regards, Ezhil --- On Mon, 9/7/09, Mohamed Lajnef wrote: > From: Mohamed Lajnef > Subject: Re: [R] Averaging rows if a condition is true. > To: "A Ezhil" > Cc: r-help@r-project.org > Date: Monday, September 7, 2009, 9:22 PM > H

[R] Averaging rows if a condition is true.

Dear All, I have matrix (5 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 wron

[R] Paired test for 2-way ANOVA

Hi, I have an experimental data with 2 factors: visit and treatment. Each subject has 2 visits and on each visit they get a treatment. We take samples before and after treatment. I can easily to do the 2-way ANOVA in R with visit and treatment as factors. anova( lm(data ~ visit*treatment) )

[R] subsetting a matrix based on condition

Dear All, I have matrix of size 2500 x 12. I would like to select all the rows if 6 out 12 values are > 0. How can I do that in R? Thanks in advance. Kind regards, Ezhil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-he

Re: [R] Extracting diagonal matrix

;- matrix(rep(1,length(A)),dim(A)[1],dim(A)[2]) > upper.tri(cmats,diag=T) > cmats[upper.tri(cmats)] <- 0 > out <- A*cmats > return(out) > } > > tril(correlation.matrix) > > will give you the output. > > HTH > > Best Regards > > Anup >

Re: [R] Extracting diagonal matrix

elation matrix, > > rep(1,100) > > :-) > > > > > > Rory Winston > > RBS Global Banking & Markets > > Office: +44 20 7085 4476 > > > > -Original Message- > > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of

[R] Extracting diagonal matrix

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

[R] Efficient calculation of correlation

Dear All, I have a matrix of size 1 x 50. I would like to calculate all possible pair-wise correlation coefficient (5x10^7 combinations) using cor(). How can I efficiently calcualte and save the result in a matrix? Thanks in advance. Kind regards, Ezhil __

[R] Calculating correlation for a big matrix

Dear All, I have a matrix of size 1 x 50. I would like to calculate all possible pair-wise correlation coefficient (5x10^7 combinations) using cor(). How can I efficiently calcualte and save the result in a matrix? Thanks in advance. Kind regards, Ezhil __

Re: [R] Problem installing R on openSUSE 10.3

em installing R on openSUSE 10.3 > To: r-help@r-project.org > Cc: [EMAIL PROTECTED] > Date: Tuesday, July 15, 2008, 9:46 PM > On Tue, 15 Jul 2008 07:08:24 -0700 (PDT) > A Ezhil <[EMAIL PROTECTED]> wrote: > > > Dear All, > > > > I am trying to install R 2

[R] Problem installing R on openSUSE 10.3

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

[R] false discovery rate !

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 value

[R] Parsing a data file - Help

Hi All, I have the data in the following format: idktsaaplahto pidg 5266199119943078A 526619921005199210302968A 19930208199302093074A 2002032920020402F322 20020402

Re: [R] Split a string of oneline into 2 lines.

Thank you very much. It works ! Ezhil --- Uwe Ligges <[EMAIL PROTECTED]> wrote: > > > A Ezhil wrote: > > Hi, > > > > I am trying to split a string into 2 separate > strings > > in 2 lines. So, tried with > > > > sprintf("%s \

[R] Split a string of oneline into 2 lines.

Hi, I am trying to split a string into 2 separate strings in 2 lines. So, tried with sprintf("%s \n %s", "ID", "Name") But R prints: [1] "ID \n Name" instead of ID Name Is it something I am missing here? Thanks in advance. Best regards, Ezhil __

[R] Scatter Plot - 3 vectors side by side

Hi, I have 3 vectors, x=rnorm(10); y=rnorm(20); z=rnorm(30). I would like to plot 3 vectors side by side (like a bar plot) with scatter plot something similar to the following: .. *** ;;; .. ** ;;; .. *** ;;; .. *** ;;; ... *** ;; x y z How can I do this with Plot()? T