In our dataset the samples/object are number of patients which is 128 and we are dealing with 12,625 genes which is our attributes of the dataset. So, it is obvious that if I calculate the correlation matrix of (128 * 12,625) the resulted dimension of the correlation matrix will be (12,625 * 12,625). I need some help about this calculation. 1. How I can make the transpose matrix of 12625 * 128 to 128 * 12625. Suppose I have written t(x) where x is a matrix of 12625 * 128. But after giving the command t(x) when I write x to see then I saw it has not been changed to 128 * 12625. 2. it is obvious that if I calculate the correlation matrix of (128 * 12,625) the resulted dimension of the correlation matrix will be (12,625 * 12,625). But I think this 12625 is huge to work with.....so is there any solution for that? What should I do now? Thanks in advance. Take care. -- View this message in context: http://r.789695.n4.nabble.com/How-to-calculate-correlation-matrix-for-128-12625-matrix-tp4631790.html Sent from the R help mailing list archive at Nabble.com.
How to calculate correlation matrix for 128 * 12625 matrix
2 messages · mahdi, R. Michael Weylandt
On Tue, May 29, 2012 at 11:26 PM, mahdi <mahdi43 at gmail.com> wrote:
In our dataset the samples/object are number of patients which is 128 and we are dealing with 12,625 genes which is our attributes of the dataset. So, it is obvious that if I calculate the correlation matrix of (128 * 12,625) the resulted dimension of the correlation matrix will be (12,625 * 12,625). I need some help about this calculation. 1. How I can make the transpose matrix of 12625 * 128 ?to 128 * 12625. Suppose I have written t(x) where x is a matrix of 12625 * 128. But after giving the command t(x) when I write x to see then I saw it has not been changed to 128 * 12625.
R functions (almost always) don't have side effects and use copy-by-value semantics so if you want to make x permanently transposed you need to write x <- t(x) which wil transpose x and then replace x with the resulting transposed matrix.
2. it is obvious that if I calculate the correlation matrix of (128 * 12,625) the resulted dimension of the correlation matrix will be (12,625 * 12,625). But I think this 12625 is huge to work with.....so is there any solution for that? What should I do now?
This seems domain specific but I might suggest you look at the Bioconductor suite and mailing list -- this is a problem they've likely faced before. Best, Michael
Thanks in advance. Take care. -- View this message in context: http://r.789695.n4.nabble.com/How-to-calculate-correlation-matrix-for-128-12625-matrix-tp4631790.html Sent from the R help mailing list archive at Nabble.com.
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.