After normalization and summarization of microarray raw data,
when I carried exploratory grouping analysis.
The samples from the two comparison groups don't cluster together, should I exclude the samples that cluster in the wrong group?
or should I continue the analysis to determine the differentially expressed genes without excluding any array?
Not only normalizing your data, you need to do all the necessary preparations on your data such as selection for training and validation before running the exploratory analysis. Go through your steps carefully,
You may not necessarily have a clear grouping or cluster due to overlap, in this case you should be able to explain such scenario based on your samples or experimental results.
Thank you Mr. Isa for your comment. I agree with you regarding the overlapping. as both comparison groups are derived from the same condition.
Dear Alaa Siddig
I completely agree with what Isa Baba Koki said. Excluding samples for such analyses, in my opinion, is never a good idea. Thanks
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