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Great answer, narrowing it down the the key points!
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The righthand plot might be totally fine once you remove that one outlier on the left, try that first. The batch effect manifesting along P…
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If it is really just two genes then why not just plotting logcounts of gene1 vs logcounts of gene2 as in a FACS scatter plot and see whethe…
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As a beginner, I hope to receive professional answers. If necessary, I can provide rewards and R code.
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Please get used to make your question reproducible and precise, meaning provide example data and reduce code to a minimum.
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