Bioinformatics Asked by Adamm on August 22, 2021
Assume that I have three different Affymetrix microarray experiments, 2x U133 (from 2015 and 2017) and 1xU133 Plus 2.0 (2019). Each array contains several different samples, some of them are common for 2 or 3 arrays. I’d like to combine these thee results to perform further MDS analysis using whole sets.
I’m aware about some batch effect that I’d like to avoid.
When I do MDS using separately normalized data from three experiments, I can see that expression pattern of sample present in two of 3 matrices is the same but the normalized signal values are raised by a certain value. It visibly affects further MDS analysis.
My questions are:
Thanks in advance!
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