Here is what I would do: use "cor" to compute the correlations extract the test part of the cor.test into a function that inputs a vector of correlations and outputs a vector of p-values. Run the new function on the correlation matrix. --Naomi At 11:19 AM 4/19/2005, xpeng wrote: >Hi Dren, > >I had the similar question, then I wrote my own C program to calculate >correlation matrices (2-3min for a 8000 x 60 matrix). You can contact with me >directly (xpeng@utk.edu), it need some extra works to get p-values. I will >post it somewhere online if there are enough interests. > >Best, >Xinxia > > > > > >===== Original Message From Dren Scott <dren_scott@yahoo.com> ===== > >Hi All, > > > >I was trying to calculate the pearson correlation (and p-value) for a gene >dataset ( 6000 rows x 10 columns). For each row vector, I wanted to calculate >the p-value with respect to the other row vectors. My resulting p-value >matrix >should be of size 6000 x 6000. > > > >I tried the iterative approach: > > > > > >for(i in 1:nrow(data)){ > > > > for(j in i:nrow(data)){ > > > > p_value <- cor.test(data[i,],data[j,])$p.value > > > > pmatrix[j,i] <- pmatrix[i,j] <- p_value > > > > } > > > >} > > > > > > > >But this will take too long for nrow(data) = 6000. Is there some method by >which I can pass the matrix into a function to get the p-values? The dataset >would also have some/many NA's. > > > > > > > >thanks, > > > > > > > >Dren > > > > > > > >--------------------------------- > > > > > > [[alternative HTML version deleted]] > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111