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I have 5 samples analyzed by EPIC V1 and 5 samples analyzed by EPIC V2, I want to analyze all samples together, But due to the differences between EPIC versions, I have some challenges;
1- How can I normalize the samples all together, however I cannot merge them in one RGset?
2- For EPICV1, although I use the package (IlluminaHumanMethylationEPICanno.ilm10b5.hg38), Still the RGset mentions the annotataion is hg19, However, EPICV2 annotation is hg38. So, is there a way to have hg38 annotation for both versions, inorder to be able to merge all samples together and get betas from common cpgs from both version?
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It sounds like you're facing significant challenges with merging EPIC V1 and V2 samples. Normalizing the data can be tricky, especially when dealing with different annotations. One approach could be to use statistical methods to adjust for batch effects and ensure consistency across versions. I had a similar experience while working on a project related to crazy cattle 3d, where merging datasets from different sources required careful consideration of their unique characteristics. Good luck with your analysis!