GMAP Signal Extraction
Signal from the GMAP microarray can be extracted using the Affymetrix Power Tool collection. This is a collection of command line tools for working with files generated from affymetrix files. These tools are freely available through affymetrix, although registration of a user account is required.
http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx
The syntax in the examples below works with version APT 1.12.0
The data files from which to extract are the cel files generated by the affymetrix instrument software (AGCC, GCOS). Several additional library files, specific to the GMAP chip are also necessary and can be downloaded here. The main library file is available in two formats
i) CDF file
ii) CLF / PGF files (both needed)
In addition, we have generated from the pgf file a series of probe files to allow extraction of specific subsets of signal from the arrays. This also includes files for the GCbin background probes that can be used for assessment/removal of background signal from the 22-mer or 25-mer probes.
| Probe Subset | Description of Subset | File |
| hairpin probes | 22mers, 3X replication | GMAP-Uts520601_hp.probes |
| hairpin control probes | (22mers, 33X replication) | GMAP-Uts520601_hpControls.probes |
| hairpin spike-in probes | 22mers, 25X replication | GMAP-Uts520601_hpSpikeIn.probes |
| all 22mer hairpin probes | probes, control probes and spike-in probes | GMAP-Uts520601_hp22.probes |
| hairpin TMM set | 17-25mers, derived from hairpin 22mers | GMAP-Uts520601_hpTMM.probes |
| human ORFeome probes | 25mers, organized into probesets with 1-8 probes per human ORF | GMAP-Uts520601_hORFeome.probes |
| human HuGene probes | 25mers, organized into probesets of 1-3 probes per human ORF, derived from the affymetrix HuGene 1.0 array | GMAP-Uts520601_hugene.probes |
| yeast ORFeome probes | 25mers, organized into probeset of 2 probes per yeast ORF | GMAP_Uts520601_hipyorf.probes |
| barcodes | 20mer DNA barcode (including all barcodes on the Tag4 array, used in the Yeast Deletion Collection) | GMAP-Uts520601_barcode.probes |
| GcBin 22mers | 22mer GcBin background probes | GMAP-Uts520601_GcBin22.probes |
| GcBin 25mers | 25mer GcBin background probes | GMAP-Uts520601_GcBin25.probes |
| Affymetrix Controls | Standard Affymetrix controls | GMAP-Uts520601_control.probes |
| All probe files | All of the above probefiles, zipped into a single file | GMAP-Uts520601_probes.zip |
Below are some examples of commands that can be run using apt to extract signal in various ways. Cel files are processed in batches and results are written to a single file, with the data from each celfile in a separate column. The cel files to be processed need to be explicitly indicated in a text file. The first line of the text file should be cel_files, then one line for each file to be processed.
eg.
filename=celfiles.txt
---------------------------------
cel_files
path/celfile1.cel
path/celfile2.cel
path/celfile3.cel
--------------------------------
path is the directory path to the celfile. It is best to use absolute paths (eg, C:/mycelfiles/)
The .