Affymetrix microarrays of different technology versions are very often used in transcriptomics analysis. Quality control and normalization approaches do exist, especially as packages in Bioconductor/R. However:
- Procedures are often different between teams.
- They are not always easy to access as they run through command lines.
- It is often not clear what the meaning of the specific settings and results are
- They are not always usable for the newer technology types of arrays.
To tackle this, we proposed an automated well-documented and user-friendly pipeline for Affymetrix microarray quality control and normalization.