Quality Control Chart Plugin
This is a plugin add-on for Dave Hancock's free microarray analysis software package
maxdView.
This plugin implements the method developed by Yongziang Fang [1], creating a control chart which can be used for
Quality Control when analyising 2-colour microarray data.
This plugin was written by Helen Hulme and is released under the terms of this
license.
This plugin will be incorperated into future releases of maxdView software.
Installing maxdView and the plugin
- If you don't already have maxdView, download and install it - its available here with installation instructions.
The plugin needs maxdView 1.0.4 or later to work.
- Right click on this plugin zip file and save to your computer using "save target as".
- Open the zip file, e.g. using Winzip.
- Unpack the zip file into the following folder of your maxdView instalation:
..\plugins\Viewer\ (If using winzip, please check the "Use Folder Names" box when extracting.)
This will create a subfolder QCChart in ..\plugins\Viewer\ contianing the class files and help files for the plugin.
- Next time you start maxdView, choose "System->Plugin Manager->Scan Plugin Folders" so that maxdView will know that it has a new plugin.
The plugin should now be available for use.
Using the plugin
In order to use the method on your data, you will need to load your data into maxdView. e.g. Use the "Import->Load plain text" option.
The QCChart works on log ratio data, or normalised log ratio data.
If your data is in raw form, then you can use the "Transform->Normalise" option or the "Transform->Simple Math" to
construct suitable new columns of log ratio values or normalised log ratio values.
Having loaded your data into maxdView, select "Viewer->QCChart" from the menu. Use the "Help" button to obtain instructions
for how to use the plugin.
[1] "A New Method for Statistical Control of Microarray Process Quality", Yongxiang Fang et al, preprint available from abrass@cs.man.ac.uk
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