Extract batch variable from GEO dataset
I want to perform gene expression analysis of the microarray dataset GSE66099. One of the steps required to move forward with the analysis is a batch correction. I want to consider measurement year as the batch variable. However, I am not sure how to extract this from the dataset. pData(gse[[1]]) didn't return any column that would contain this information. They only have a submission date. Can someone help me figure out how to extract the batch variable?
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Most likely this does not exist as it is not mandatory to include it. You would probably be better off simply doing a PCA and see whether this shows some evidence for batch factors that require correction.