Replicates in DESeq2
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leo.dagata • 0
@bcdc7141
Last seen 5 days ago
France

Hello everyone,

I would like to know if you could help me about someting in DESeq2.

In the documentation, they talk about technical replicates ad biological replicates. From what I understand:

  • biological replicates are for example samples that do not come from the same people/animal/cellular culture.
  • technical replicates are for example samples that were sequenced twice on the same or on different machine.

After discussion with other bioinformatician and biologist, it appears to me that sometime we do not have the same consideration of the term "biological replicate". Indeed, If I make some swab from the same animal, does it results in technical replicate (because they come from the same individual) or biological replicates ? (because it's not exactly the same sample that is sequenced twice).

I hope my question is enough clear.

Thanks

Léo

DESeq2 • 163 views
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@mikelove
Last seen 1 day ago
United States

A better definition for technical replicate for our purposes [that is, to justify adding the samples together in DESeq2] is: additional sequencing of a prepared library.

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Hi Michael,

Does it means that is it possible to compare for example one treated animal against one untreated animal if I have 2 samples of each animal (and so 2 different library preparation for each animal) ?

For me it does not really reflect the biological variability that DESeq2 requires for the differential testing step. What is your definition of biological replicates?

Thanks,

Léo

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That experiment doesn't make sense to me, because you aren't observing the key variation which is how the treatment effects different organisms.

So just because it is not a sequencing technical replicate, doesn't mean it provides sufficient biological replication to make inference on the condition effect.

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Does it means that is it possible to compare for example one treated animal against one untreated animal if I have 2 samples of each animal (and so 2 different library pirlo tv apk pure preparation for each animal) ?

For me it does not really reflect the biological variability that DESeq2 requires for the differential testing step. What is your definition of biological replicates?

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No, I wouldn't say that you have sufficient information to talk about organism differences if you have two organisms, one from each condition. You've only observed within-organism variance but have no evidence of across-organism differences separate from the condition effect. This seems pretty clear to me though, is there a remaining question?

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