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how can I do expression analysis when there is no replicate and no control

I am wondering if one knows which method is a correct way to go with such a data I have 4 conditions where I obtained the microarray data. I don't have a control and all 4 conditions are treated ones. I want to know which genes are changed in each condition in comparison to the rest.

So imagine I have a matrix of 4 by 18000 (4 samples and 18000 genes).

gene
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written by Learner Learner

I think you should add the "no control" part to your title too. This might turn out to be quite challenging as these are merely 4 data points and there is no accounting for the underlying distribution whatsoever.

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written by Ram Ram

@RamRS yes, I added it in the title. actually some suggest to perform permutation, some simple t test ... but it is really confusing !

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written by Learner Learner

Please search both Biostars and the web for opinions on how to deal with underpowered (=no replicates) data. This question has been asked many times before, and you'll find a lot of good answers. The short answer is: Any analysis will not be statistically sound and results will serve only for exploratory purposes.

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updated by Ram Ram • written by ATpoint ATpoint

Hello Learner !

We believe that this post does not fit the main topic of this site.

Received opinions on Bioconductor by two statistics experts, clarifying that unreplicated data are of little use: https://support.bioconductor.org/p/117407/

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by ATpoint ATpoint

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