GNF Publication: MOID

Match-Only Integral Distribution (MOID) Algorithm for
High-Density Oligonucleotide Array Analysis

Yingyao Zhou¹ & Ruben Abagyan²

¹ Genomics Institue of the Novartis Research Foundation, San Diego, CA USA.
² Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA USA.

BMC Bioinformatics 2002, 3:3 (22 January 2002)
[Abstract] [PDF]

Raw data, Affymetrix CEL files:
11 Hu6800 Arrays, 21 Hu35KsubA arrays and 2 Mu11KsubA arrays.
Raw data, TXT files:
here Format for the TXT files: Gene,PM1,MM1,PM2,MM2,...
Notice the size of probe sets are different.
Sample description, MS Word DOC.
Chip description, old Affymetrix 1lq files:
Hu6800 Array, Hu35KsubA and Mu11KsubA array.
Chip description, txt files:
Hu6800 Array, Hu35KsubA and Mu11KsubA array.
Format for the txt files: this is a tab-delimited file, four column: name (probe set name), px, py, mx, my (x,y coordinates for PM probes and MM probes, respectively). px, py, mx, my are comma-delimted strings.
E.g., the first probe set in Hu6800.txt is:
A28102_at 5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24 2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2
This means A28102_at has PM probes at (5,1), (6,1), (7,1), ... and MM probes at (5,2), (6,2), etc. So far Affymetrix always put a MM probe right beneath a PM probe (which means if there is a PM probe at (px, py), there must be a corresponding MM probe at (px, py+1)). You can use the (x, y) coordinates to find the raw intensities in the CEL files (which contains five columns X, Y, MEAN, STDV, NPIXELS. MEAN is the intensity column.)
Results for MAS4 - MOID comparison on 366 spiking data, here.