I'm calculating correlations between two matrices
mat1 <- matrix(sample(1:500,25), ncol = 5, dimnames=list(paste("mat1row", 1:5, sep=""), paste("mat1col", 1:5, sep=""))) mat2 <- matrix(sample(501:1000,25), ncol = 5, dimnames=list(paste("mat2row", 1:5, sep=""), paste("mat2col", 1:5, sep=""))) using what would seem to be two similar methods: Method 1: > f <- function(x,y) cor(x,y) > apply(mat1, 1, f, y=mat2) Method 2: > cor(mat1, mat2) However, the results (see blow) are different: > apply(mat1, 1, f, y=mat2) mat1row1 mat1row2 mat1row3 mat1row4 mat1row5 [1,] -0.27601028 -0.1352143 0.03538690 -0.03084075 -0.60171704 [2,] -0.01595532 -0.3881197 -0.43663982 0.49081806 0.33291995 [3,] 0.35969624 -0.0582948 0.57462169 0.09926796 -0.02948423 [4,] -0.41435920 -0.7164638 -0.21213496 -0.55183934 -0.25341790 [5,] 0.33802803 0.5371508 0.05219095 0.83533575 0.17850291 > cor(mat1, mat2) mat2col1 mat2col2 mat2col3 mat2col4 mat2col5 mat1col1 -0.84077496 -0.01538414 -0.6078933 -0.2263840 -0.1421335 mat1col2 0.23074421 0.54606286 -0.2354733 0.5214255 -0.2129077 mat1col3 -0.80000528 0.19550100 -0.5920509 -0.8694040 0.6853990 mat1col4 0.08050976 -0.55449840 0.6225666 0.6187971 -0.8971584 mat1col5 -0.10199564 -0.43854767 -0.5803077 -0.5100285 0.2848351 Also, for method 2, the calculations are done on a column x column basis. Is there any way to do this on a row by row basis. Looking at the help page for cor, I don't see any parameters that could be used to do this. Thanks, - Bruce
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