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I have 10 microarray series(GSE IDs).Each series correspond to a disease. However , the control is same in all the 10 conditions but generated by different groups. How to go for a combat here? I have a problem in designing mod.matrix in the case. Further, I just want to remove the variation due to batch effects and I want to retain the variability due to biological conditions, which is of my prime interest.
Please help me regarding this.