DESEQ2 Batch Effect
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sap275 ▴ 10
@1a70038b
Last seen 5 weeks ago
United States

Hello! Hoping I could find some answers here. I have this experimental setup shown in this image:

enter image description here

I was wondering using the formula design = ~ batch + condition would be sufficient enough to control for batch effect considering the fact that the control group is not represented in the other batch. How should I proceed with further analysis? Surprisingly, Limma was able to somewhat correct the data to cluster broadly by condition. I am stuck on what to do.

I will appreciate any answer. Thank you so much!

DESeq2 BatchEffect RNASeq • 339 views
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swbarnes2 ★ 1.3k
@swbarnes2-14086
Last seen 1 hour ago
San Diego

Nope. Batch is entirely confounded with day. You will have no way at all of knowing what day 4 changes are not batch effects.

What does that date represent exactly? Because date of illumina run will add no artifacts. But if that date represents anything else, then you are in trouble.

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The "batch" is our isolation date for RNA seq, while "day" is the dates we obtained our samples.

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Different isolation days will cause a, batch effect. Next time, the experiment needs to be planned more carefully.

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