Hello, I have performed a microarray experiment using the Affymetrix CytoScan HT-CMA 96F kit and currently have 96 .CEL files. Using the RHAS software, I am able to convert these CEL files into .CHP/RHCHP files and then use CHAS to export the results as .AED files. However, both RHAS and CHAS are Windows-based applications, and I would prefer to perform the entire workflow on Linux, ideally via command-line.
I have access to all required library files for the kit, including the CDF, specialSNPs, chrX/chrY probes, etc. I am wondering:
Is it possible to perform the full analysis on Linux using APT (Affymetrix Power Tools) to generate .AED files directly or indirectly?
If APT does not support AED export, are there any alternative tools or workflows available on Linux that can produce AED-equivalent output?
Ultimately, my goal is to convert .CEL files into .AED format using Linux, without relying on Windows-based tools.
Any guidance or suggestions would be greatly appreciated. Thank you!
