Index of /goldenPath/misc/transcriptome.affymetrix.com/download/phase2/raw_data

README

This directory consists of data files for one of the eight cell lines used in the RNA transcript map experiments for Phase 2 of Affymetrix/NCI Human Transcriptome project.
RNA samples were hybridized to 3 replicate arrays.
Data for the 'SK-N-AS' cell line is hosted here.
Ten Chromosomes (6, 7, 13, 14, 19, 20, 21, 22, X, Y) span 98 chips.
There are a total of 294 files in this folder (98x3=294)
The filenaming convention for these files is as follows:
- cellLine_replicate_chipnum.gz
- SK_1_27.gz => SK cell line, replicate #1, chip #27
Phase2 chips were designed from DNA sequence of Human Genome version 30 of NCBI. (June 2002 release)
The chromosomes that appear on a given chip can be found in the file "phase2_chip_mapping.txt". This file is also located in this directory.
Each file has 14 tab seperated values. They are as follows:
- pm probe sequence: 25mer sequence
- sequence top strand: t/f (true/false)
- sequence name: name of chromosome
- sequence position: position of first base of the probe sequence on chromosome
- pm x: x value of pm feature on chip
- pm y: y value of pm feature on chip
- mm x: x value of mm feature on chip
- mm y: y value of mm feature on chip
- pm intensity: intensity of pm feature
- pm sd: standard deviation of pixel values in the pm feature
- pm npixels: number of pixels in pm feature
- mm intensity: intensity of mm feature
- mm sd: standard deviation of pixel values in the mm feature
- mm npixels: number of pixels in mm feature