Is it correct to merge two raw CEL datasets and then perform quality control, background correction, and normalization on it?

1

Hello, biostars.
I have raw CEL files of two microarray datasets that I read them in R by the ReadAffy function and finally, I want to remove the batch effect between them. I want to know if is it correct to merge these two datasets at first and then perform quality control , background correction, and normalization and then perform batch effect removal? Or I should perform quality control , background correction, and normalization separately for each dataset at first then merge these datasets and remove the batch effect?


R


affymetrix


qualitycontrol


microarray


batcheffectremoval

• 45 views

updated 2 hours ago by

★

1.9k

written 9 hours ago by

▴

20



Source link