Hi Jeffrey, I think this is because you are passing 'normalize.quantiles' a matrix of integers, while that function expects a matrix of doubles: > print(normalize.quantiles(y)) [,1] [,2] [1,] 8.360796e-270 8.360796e-270 [2,] 9.980857e-264 9.980857e-264 > print(normalize.quantiles(y+0)) [,1] [,2] [1,] 1.5 1.5 [2,] 3.5 3.5 Probably the affy people should add an integer->double conversion to their R wrapper code for normalize.quantiles. (e.g. see last lines of vsn/R/getIntensityMatrix.R) Best wishes Wolfgang Jeffrey Chang wrote: > 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 > -- ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber