Hi all,
I have a question concerning microarray normalization followed by batch correction.
I have a single experiment with patient data on two time points and I would like to compute the differential expression between both time points.
The samples were analysed in 2 batches.
Batch 1 contains 32 samples (16 on time point 1 corresponding with 16 on time point 2), batch 2 contains 80 samples (40 on time point 1 corresponding with 40 on time point 2).
8 samples (4 pairs) were measured in both batches.
I would like to normalise my data using RMA, followed by a batch correction based on the 8 samples analysed in both batches using the SVA ComBat function with batch number as covariate.
However, it is not clear to me whether I need to perform RMA on both batches separately or on all data together before executing the ComBat function.
Thanks in advance for any help!