Hello,
One of the most helpful posts I've seen on BioStars is this post that links to a fabulous tutorial on analyzing Affymetrix microarrays: Analysing Microarray Data In Bioconductor
It has helped me so much, but as far as I can see online, there is not an agreed-upon, straightforward workflow for analyzing any microarrays not made by Affymetrix. There are some GEO datasets that use Illumina microarrays (Sentrix Mouse-6, MouseWG-6, MouseRef-8, etc) or Agilent arrays (Agilent-012694 Whole Mouse Genome G4122A) and do not come with .CEL files.
Are there are any accepted workflows for analyzing these data? If so, I would love to be pointed to them.
Thank you in advance, BioStars!