When running ChAMP pipeline, the step SVD.plot initially gives no batch effect but after running 5-6 times with the same data it is giving batch effect. Is this possible..????
Another problem is that at step myDMP, in the argument adjPVal, changing the cutoff and running the pipeline with the same cutoff gives different number of significant MVPs when the pipeline is repeated 3-4 times. Also running on different system gives variable results I don't know whether how this is possible that the same pipeline with the same setting gives different results when run repeatedly.
Anyone having the same issue or have any solution for this problem is highly appreciated.