After some struggling with the data format, non-standard in BioConductor, I have gotten cor.balance in package CORREP to work. My desire was to obtain maximum-likelihood p-values from the same data object using cor.LRtest, but it appears that this function wants something different, which I can't figure out from the documentation.
Briefly, my dataset consists of 36 samples from 12 conditions and I have 497 genes of interest to be correlated. The following works: M <- cor.balance(stddata, m = 3, G=497) The following does not: M.p <- cor.LRtest(stddata, m1 = 3, m2 = 3) Do I need to do something to stddata between example 1 and 2 or does "m" stand for something different in the two examples? sessionInfo follows. Thanks, Mark > sessionInfo() R version 2.7.0 Under development (unstable) (2008-03-05 r44683) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] grid tools stats graphics grDevices datasets utils [8] methods base other attached packages: [1] rat2302_2.0.1 Rgraphviz_1.17.13 graph_1.17.17 [4] igraph_0.5 CORREP_1.5.0 e1071_1.5-17 [7] class_7.2-41 affy_1.17.8 preprocessCore_1.1.5 [10] affyio_1.7.13 Biobase_1.99.1 loaded via a namespace (and not attached): [1] cluster_1.11.10 -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 204-4202 Home (no voice mail please) mwkimpel<at>gmail<dot>com ______________________________________________ R-help@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.
