Hello everybody, I'm using the normalize.quantiles function from the "affy" package version 1.3.27, using R 1.8.1 on Mac OS X. I'm seeing some unexpected behavior when I try to normalize data read from a file. I have a data file called "test.dat" containing: ------------- 1 2 3 4 ------------- When I execute the code: ------------------------------ library("affy") x <- read.table("test.dat", header=FALSE) y <- as.matrix(x) z <- matrix(c(1, 3, 2, 4), 2, 2) print(normalize.quantiles(y)) print(normalize.quantiles(z)) ---------------------- I get very strange results from the first print statement. > source("test.R") [,1] [,2] [1,] -1.067217e-314 -1.067217e-314 [2,] 1.384441e-291 1.384441e-291 [,1] [,2] [1,] 1.5 1.5 [2,] 3.5 3.5 > The values for the first normalization changes when I rerun it, so I suspect it might be caused by an invalid pointer dereference. The normalize.quantiles is implemented in C in qnorm.c/R_qnorm_c. Unfortunately, I don't know how R passes around matrices around, so I cannot easily trace the problem further. Has anyone seen this before? I have attached the files "test.R" and "test.dat" containing the data above. Please let me know if mailman has stripped it, and you would like me to send you a copy. Thanks, Jeff -------------- next part -------------- A non-text attachment was scrubbed... Name: test.dat Type: application/octet-stream Size: 8 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040131/98dabf58/test.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: test.R Type: application/octet-stream Size: 171 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040131/98dabf58/test-0001.obj