THE AFFYPROBEMINER WEB SITE
The original AffyProbeMiner web site was lost sometime in mid-2011.
We are now able to provide only a download of the unix/linux command-line code that allows the user to generate the altered mapping files.
!!!YOU MUST DOWNLOAD THE APPROPRIATE BLAT EXECUTABLE FOR YOUR OPERATING SYSTEM!!!
The BLAT executable for your platform can be downloaded from http://hgwdev.cse.ucsc.edu/~kent/exe/
I used http://hgwdev.cse.ucsc.edu/~kent/exe/macIntel/blatSuite.zip for my intel mac
I deleted the version of blat that pre-exists in the proberedefine subdirectory of the affyprobeminer download, and replaced it with blat from the blatSuite download
In the README file there is a test example given:
./generatecdf.SH testchip "Homo sapiens" ccds transcript 0 5 0 testdata targetsequence
I successfully ran that test example on my intel mac in early October 2011, using the appropriate version of BLAT.
The full text pdf of the original AffyProbeMiner publication can be accessed at http://bioinformatics.oxfordjournals.org/content/23/18/2385.full.pdf
Please contact me firstname.lastname@example.org with any problems or comments.