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Counts plot does not match fold change between groups

Hello all,

I have patient data that are grouped based on a characteristic. I ran DESeq2 between the two groups following the tutorial. Everything seems fine but when I plot one of the top differentially regulated genes using plotCounts(), it seems the difference is driven by few outliers. Here is one example that DESeq2 outputs more than 6 log2FoldChange that is highly significant:

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I would appreciate if you can help me understand this issue. My feeling is that the counts are not normalized so it may not show the difference?

Thanks

rna-seq deseq2
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updated by jordi.planells jordi.planells • written by juara • juara

2 answers

Driven by outliers or not, (you really want to say that 3/7 samples are outliers?) the two sets of samples pretty clearly have different means, so the software was right to flag that.

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written by swbarnes2 swbarnes2

Have all the sequencing libraries been processed equally? Do they come from the same run? Maybe you have a batch issue there.

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written by jordi.planells jordi.planells

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