Analyzing non-Affymetrix microarrays

Question

[randalljellis]

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!

Answer 1

[igor]

If the data is in GEO, you can try using GEO2R for analysis. That will perform the analysis, but also give you an R script so that you can do it yourself.

Answer 2

[Antonio R. Franco]

You don't mention how you want to analyze the data, but if using limma, the vignette contains examples of how to use Agilent text data.

In this case, you will be alerted for the situations of using one or two colors, and if a within / between normalization of both types of normalization is required.

I found that it was easy to follow