removal batch effect
Dear all Can I use SVA package to remove batch effect before I combine RNA-seq data of different studies? Each study have biological replicates. Which packages are highly recommended for this purpose? The best
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swbarnes2
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l.nazari •
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l.nazari •
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This cannot be answered without seeing a table that shows which samples belong to which study and experimental group. Can you add this? You must make sure that every condition has replicates in each dataset.
Also, note that for finding DE genes, the typical way to handle batches is not to alter the counts in anyway, but to leave them as they are, and include batch as an element of the design.