Analysis with Batch correction
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@b295d7f1
Last seen 10 months ago
Italy

Hi there!

I am performing differential expression analysis on embrionic cells. According to PCA (see below), I have found that samples are clustering according to Experiment day and not by Condition

enter image description here

Then, I have performed in parallel the analysis

  • taking all samples
  • taking all samples and corrected by the batch effect
  • taking samples processed only at day 27th
  • taking samples processed only at day 21th

When I have compared the obtained results, I have found that the 4 analyses have a low number of DE genes(see venn diagrams below).

enter image description here

I was wondering how the results of all analyses show low concordance and which one of these analyses reflects more the biological truth.

Best regards,

Giulia

DESeq2 BatchEffect • 450 views
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@mikelove
Last seen 2 hours ago
United States

The recommendation would be design=~batch + condition. If there are low DE number that is nevertheless the correct approach.

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