Correcting partially penetrant batch effect
Entering edit mode
swbarnes2 ▴ 710
Last seen 9 hours ago
San Diego

I have a control set of samples, and 3 viruses, each exposed to two treatments. 5 replicates of each. In two viruses, in both treatments, the first two replicates are left shifted in the PC1 values compared to the other replicates, example:

  • virus1_treatment1_Rep1 -26.21084691
  • virus1_treatment1_Rep2 -23.81517717
  • virus1_treatment1_Rep3 -13.52695811
  • virus1_treatment1_Rep4 -10.74887635
  • virus1_treatment1_Rep5 -10.11061144

but in the controls, and the third virus, all 5 replicates look the same. I have results using a design of ~ virus_treatments + replicate, but I was wondering if that was right when the replicate effect is so different between the different viruses.

Is there a better way to deal with this?

DESeq2 • 87 views
Entering edit mode
Last seen 13 hours ago
United States

Not really, the whole point is that the replicates account for within group variability. You can always access quality of a sample through independent measures, and then exclude on objective criterion.


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