DESeq2 or EdgeR or Limma without replication

Hello, I am trying to do different expression using DESeq2, or EdgeR, or Limma but it always obtain error.
Can I use these tool without replication? Cause patient sample, for one condition I only run 1 time.
Help me please!
Thank you so much!

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Welcome, @ngutrinh

I’m not quite sure what you mean – if you only have a single dataset, then there would be nothing to compare for expression differences (?). Perhaps I am misunderstanding. That is Ok – the short answer is that replicates are required when using these tools in Galaxy.

We found that many usage issues, false errors, and unexpected results were avoided by requiring replicates by default. Even the original tool authors only recommend using the tools without replicates for very limited “exploratory” purposes only – not analysis.

FAQ: Extended Help for Differential Expression Analysis Tools

The FAQ includes a link to the Bioconductor forum where there is much discussion about their strong recommendations about use of replicates with their tools. Punch line: not using replicates produces invalid results (…if the job completes at all…).

I hope that helps!

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Thank you so much for your reply Jennaj,
I have 3 different groups but each group only have one RNA-seq data, and I tried the tools and got error. Following your answer, each groups should have replicated. Thank you!

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I have used DESeq2 without any problem. I have triplicates for each factor. I use feature counts to extract the reads. Then I cut the columns to have geneID and reads. Basically 2 columns. Then you can select triplicates for each factor. It was working… Thanks… Nagul

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