DGRC Basic Hybridization Analysis (DGRC_BHA)
The DGRC Basic Hybridization Analysis (DGRC_BHA) is an R program that gives users a quick and easy way to evaluate the quality of the results extracted from DGRC microarrays. Basic Hybridization Analysis looks at the intensity values extracted from a GenePix results (gpr) file and creates an html file that contains statistics about the intensity values of spots on the microarray and various plots common to microarray analysis like MA-plots.Script Output
The R script outputs a large amount of information based on your hybridization results, including:
- Mean, median, and standard deviation of foreground, background, and positive and negative controls
- Spiking control results
- Heat plots of foreground, background, M, and A
- Summary of flagged spots
- Channel vs channel plot
- Histograms of foreground and background
- Histograms of M and A before and after OLIN normalization
- MA plots before and after OLIN normalization
- Tables listing spots with the highest and lowest M before and after OLIN normalization
- The OLIN normalized data can be exported as a tab-delimited file.
We have written a variety of guides to assist users in installation, instructions for use, and explanations of output
|Installation Guide and
Use of DGRC_BHA
This is a guide detailing how to install the R package and necessary plug-ins on Windows, and how to use the DGRC_BHA script.
(R runs on FreeBSD, Linux, Windows, and MacOS.)
This is a ppt file detailing how to install the R package and necessary plug-ins on Windows, and how to use the DGRC_BHA script.
(Requires a program capable of running .ppt files.)
Copyright 2005 DGRC
The actual R-script used to run the analysis.
|Guide to judging quality of a hybridization||
This guide is meant to explain the output of the DGRC_BHA script and help you interpret the quality of your hybridization
An example of the output generated by the DGRC_BHA script.