I have two different ChIP-seq data for different proteins, I have aligned them to some fragments in the DNA. Some of these fragments get zero read count for one of them or for both. To be able to say these fragments has protein X much more than the protein Y, I use student's t-test.
I wonder if It would be better to remove the zero values from both of the data showing rpkm values for each fragment. Moreover, they pose problem when I want to use log during data visualization part.
What would you suggest?
No.. remove data only if it is a known blunder, etc. Otherwise it's telling you something that you need to understand. Your convenience and the operations of nature does not have to be the same. In science Nature Rules not your convenience.. David Booth PS one solution to the problem of zeros in further.analysis.may be to ask a second question here. Best wishes David Booth
Could you please check my other question (https://www.researchgate.net/post/How_to_normalize_one_data_according_to_another_data) ?
Thanks a lot David Eugene Booth
I'm going suggest that you contact Dr Jochen Wilhelm also on Researchgate for your second question. He knows more about that than I do. Best wishes Good luck with your research, David Booth
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