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3.3 years ago
Gene_MMP8
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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?
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.