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Old 03-10-2015, 01:10 PM   #6
Simon Anders
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Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994

Could it indicate a mislabeling of the samples? I am suspecting this already from the PCA plot of VST values.
Yes, your PCA plot shows that something is amiss, but this has nothing to do with what I discussed above.

You need to figure out what the difference between the sample groups to the left and to the right is. Maybe there is some mislabelling, but it would have to be a rather catastrophic one, not just a single mislabelled sample. Or there is some dramaticv batch effect, such that something in the processing was done very differently in the left sample group than in the right one.
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