I have to perform differential gene expression analysis using limma. Can I use GEO Series Matrix File(s) (expression set) in the limma workflow (differential expression analysis) without actually extracting the expression set from raw .CEL files. As I can see that limma workflow involves rma() correction before extraction of expression set but I can't find any information that states whether the GEO Series Matrix File(s) (expression set) is pre-processed or not.
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Can I use GEO Series Matrix File(s) (expression set) in the limma workflow (differential expression analysis) without actually extracting the expression set from raw .CEL files.
Generally, yes, but GEO does not guarantee that each series matrix file will be normalised and log2-transformed. You should check via a box-and-whiskers plot and a histogram.
For each microarray study, there will also typically be a blue Analyse with GEO2R button on the main accession page. If you follow that and then click on the R script tab, you'll find code that allows you to pull the data automatically.
Kevin
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