Packed file with the main R scripts: the MicroArray scripts and the process_arrays.r script.
merge.r [view]
This is a modified version of the process_arrays.r script which may be used to merge data series from two different array designs.
qc.r [view]
This script contains some simple quality control plots.
sample_arrays.dat [view]
Sample-array matching annotation file for the GSE44666 GEO data series.

Agilent array design annotation files

Agilent array design annotation files can be obtained from Agilent eArray which annoyingly requires registration, and may not function in all browser. To find the annotation files in eArray, log in, go to Microarray, Browse Microarray Designs, and then identify the array design you want annotation files for. Select download for this, and then you can choose which annotation files to download. I have for the most part used the Gene list (filename contains GeneList) file, but you could alternatively get the All annotations (filename contains AA) file. These annotation files tend to have names on the form [DesignID]_D_[type]_[versiondate].txt.

If you have difficulty getting eArray to work or finding the appropriate files, please send them an email and ask for assistance: they deserve the trouble when they are making it this inconvenient to get to the annotation files!

Last modified November 05, 2014.