I am performing differential methylation analyses on different subgroups of a patient population. The data was assayed on Illumina EPIC arrays. We have considered using combat for the batch effects, or just blocking in limma as previously discussed on this forum.
I have a question however regarding SVA and a singularity issue with one particular subset. It seems that there is only 1 sample on several of the plates, and 1 sample in the wells. I tried merging the samples and running the SVA model again. The singularity error message remained. I have now been considering running the model + batch effects with SVA on the entire targets sample, and then extracting the subsets afterwards. Would this "fix" lead to false estimates in the downstream analyses? It seems I need a larger dataset in order to avoid those single samples on the plates and the wells.
Thanks for your input.