Hi list. I am having problems with carrying out quantitative analysis with samr. I am trying to correalte gene expression across a microarray data set with weight loss. My expression data is in the form of a matrix and my weight loss data is in the form of a vector. Toy examples (but real data) follow. #expression data wld2 V1 V2 V3 V4 V5 [1,] 7.90 7.57 7.45 8.09 7.67 [2,] 7.60 7.23 7.17 7.64 7.21 [3,] 8.24 7.78 7.67 8.29 7.75 [4,] 9.60 9.18 9.08 9.71 9.20 [5,] 9.31 8.93 8.79 9.39 8.97 class(wld2) [1] "matrix" wlv2 wlv2 [1] 16.5 17.1 8.1 22.4 0.0 class (wlv2) [1] "numeric" The two other parameters are a character list of geneids and a character list of genenames. I have put these components together as detailed in the samr vignette. d=list(wld2, wlv2, geneid, genenames) And attempted sam anaylsis as follows: sam.obj <- samr(d, resp.type='Quantitative', nperms=100) This fails with the following errors: Error in x %*% yy : requires numeric matrix/vector arguments In addition: Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' I know that %*% is the matrix multiplication operator but my x (wld2) and y (wlv2) values are defined as they should be (matrix and vector respectively) and I cannot track down my mistake. Can anyone help? Thank you - session info follows. Iain R version 2.6.2 (2008-02-08) i486-pc-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB .UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] biomaRt_1.12.2 RCurl_0.8-3 samr_1.25 [4] impute_1.0-5 affy_1.16.0 preprocessCore_1.0.0 [7] affyio_1.6.1 Biobase_1.16.2 loaded via a namespace (and not attached): [1] rcompgen_0.1-17 XML_1.93-2 [[alternative HTML version deleted]]