search for: ezhil

...ill 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, 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

...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 ____________________________________________________________________________________ TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV.

...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

...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 about the same missing library. I don't know what I have to do now. Could please help me fixing this? Thanks. Best regards, Ezhil

...sponding mapping in B (mRNA, say, m1,m2,m3) and I would like calculate correlations between p1-m1, p1-m2, and p1-m3 and then for the second variable p2 etc.  I have the mapping information in another file (annotation file). Could you please suggest me how to do that? Thanks in advance. Kind regards,Ezhil   [[alternative HTML version deleted]]

...w it looks like Robert c("90", "50", "30") John c("91", "20", "25", "45") How can I get rid off c("", ..)? In my file, I would like to have Robert 90, 50, 30 John 91, 20, 25, 45 Thanks in advance. Regards, Ezhil

..."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 this. I would greatly appreciate any help in doing this. Thanks in advance. Kind regards, Ezhil

Dear All, I have a matrix of size 10000 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

...print (reformat) this vector as: 001100000000001111111111111111111111111111111111 by simply removing the spaces between them. I have been trying with many option but not able to do this task. I would greatly appreciate your suggestion on fixing this simple task. Thanks in advance. Kind regards, Ezhil ____________________________________________________________________________________ Bored stiff? Loosen up...

...; sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks in advance. Kind regards, Ezhil

...sified 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. Kind regards, Ezhil j <- 1; n <- dim(dat)[1]; cat <- as.character(dat[,1]); row <- matrix(nrow=nrow(dat), ncol=ncol(dat)); for(i in 1:n-1) { if(cat[i] != cat[i+1]) {row[j, ] <- dat[j, ]} else { start <- j; end <- i; } row[j, ] <- colMeans(dat[j:i, ]); j+1;...

...ptions I should use? (2) my prof. asked me to add '*' above the boxplot, if the comparison is significant. How do I add this '*' in the boxplot? I used: anova(lm(obs ~ treat*time, data=table)) for finding significance. Any help is greatly appreciated. Thanks in advance. Regards, Ezhil

...;- apply(dat,1,aof) Now, how can I use 'glht' for the above amod. I know that I cannot use simply glht(amod, linfct = mcp(f = "Dunnett")). Also, if I want to use Dunnett for comparing C vs (T1 and T2), how can I specify this in the glht function. Thanks in advance. Regards, Ezhil

...all the main and interactions effects. If I want to perform postdoc test on one of my main effects, say T, what method I should use (i have unequal sample size)? Is there anyway I can extend my above '3aof' function to do this? I greatly appreciate your help. Thanks in Advance. Regards, Ezhil Ph.D Student School of Biotechnology AU, India.

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 mean of the first 4 rows of the old one, the second row of the new matrix to be the mea...

...w it looks like Robert c("90", "50", "30") John c("91", "20", "25", "45") How can I get rid off c("", ..)? In my file, I would like to have Robert 90, 50, 30 John 91, 20, 25, 45 Thanks in advance. Regards, Ezhil

...OVA with 3 factors: individuals (3), time(3) and treatment(2). I tried something like, fit <- lm(dat ~ ind*time*treat) res <- anova(fit) Is this the correct approach? Is there any R pacakge to calculate P values using permutation for ANOVA with 3 factors? Thanks in advance. Best regards, Ezhil

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