RAIDA 2014 General Usage Notes ------------------- RAIDA works on the 64-bit R, a free software programming language and software environment for statistical computing and graphics. Dependencies: ------------ To run RAIDA, the following packages are required: MASS, protoclust and limma. Optionally, qvalue if the q value is used for a multiple test correction. Description of input parameters: ------------------------ raida(c.data, n.lib, show.ref.features=FALSE, show.all.features=FALSE, zsc=0.00) - c.data = count data - n.lib = numbers of samples in two conditions (e.g., n.lib=c(15,15)) - show.ref.features = whether to show the features found as the common divisor. The default is FALSE. - show.all.features = whether to show a feature with less than 20% of nonzero counts in each of both conditions. The default is FALSE. - zsc = the value for the epsilon in a modified ZIL model. The default is the minimum of nonzero ratios. Example: ------- source("raida.R") dat = read.table("example.txt", sep="\t", header=T); result = raida(dat, n.libraries); result[result$p.adj<0.05,]; Disclaimer ------------------------------------------------------------------------------- Copyright (c) 2014, Michael B. Sohn, GIDP Statistics University of Arizona THE R SCRIPT FOR RAIDA IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO RAIDA INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF RAIDA.