Hello, starting from a txt file with count data, I am analysing RNAseq data from three different independent experiments which should be merged into a single analysis. Sample characteristics, such as disease conditions, are perfectly confounded within the batches. The use of housekeeping genes, such as those suggested by Eisenberg et al. (http://dx.doi.org/10.1016/j.tig.2013.05.010), could be one way of addressing the batch effects. Is there a way in JMP Genomics which allows specifying sets of genes which could be used to adjust the batches?
Thank you so much for your time.
