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Please provide any feedback you care to about the software described below. Send me email at sdavis2@mail.nih.gov.

ACME Bioconductor Package

This is software for the R programming environment that calculates enrichment of signal associated with chIP/chip experiments. It uses a moving window to calculate the amount of regional enrichment based on a chi-square test. The software is currently designed to work with NimbleGen? tiling arrays and reads the .gff files generated by the NimbleScan? software.

Installation

The ACME package is now available as part of the Bioconductor project. Please visit Bioconductor for installation instructions and help on usage.

Test files

gff.test.files.tar.gz: A couple of GFF files for testing (hg17)

doNorm

This is a simple R script for normalization of DeArray Result files.

Installation

1. Install x11 and xCode (on a Mac)
2. Install the R program from the R homepage
3. Start the R program
4. Install a few add-on packages:
   1. R.utils
   2. limma
   3. Biobase
   4. tcltk
   5. tkWidgets

Basic Usage

1. Start the R program
2. Click the "X" button on the R window to start the X-windows system
3. Type (or cut and paste) the following:

   source('http://watson.nci.nih.gov/twiki/pub/Main/SoftwareTools/normalize.R')
   doNorm()

4. Choose the files that you want to normalize
5. Choose the directory into which to store the (many) files