process-affymetrix-cel-files.md

Process Affymetrix CEL Files

1: Create Marker Positions step [affy-markers] must have been run already or must be selected

2: Directory with Affy Power Tools executables (should contain apt-probset-genotype, etc. Available at http://www.affymetrix.com/)

These files begin with apt-, such as apt-probeset-genotype. [edit this step name, wrong website, not sure of actual tool name, etc. JZ will look into this]

3: Directory with Affy Power Tools library files (should contain GenomeWideSNP_6.cdf, etc. Available at http://www.affymetrix.com/)

These files begin with GenomeWideSNP_6, such as GenomeWideSNP_6.cdf.

4: A target sketch file (such as hapmap.quant-norm.normalization-target.txt)

[explain this file...] This file is on MSI, not sure if it's part of Genvisis resources...

5: (optional) Use the full affymetrix cdf, which contains more mitochondrial probesets

This option may be of interest if you are examining mitochondrial DNA copy number.

6: (optional) Sample name override file containing the following two columns: CurrentID, DesiredID

7: Number of threads