Question

DEG without replicates

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4.5 years ago

mursyidahkhan • 0

Hello everyone. I have transcriptome data from 2 samples but both samples do not have replicates. I tried EdgeR but the comparison failed due to no biological replicates. I could not use Blast2Go since it's not a pro version. Anybody has any suggestion on how to proceed with DEG without replicates.Thanks in advance.

RNA-Seq • 996 views

ADD COMMENT • link updated 4.5 years ago by swbarnes2 14k • written 4.5 years ago by mursyidahkhan • 0

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Please use the search function for previous threads on both Biostars and the web. This has been discussed many! times before and fairly many suggestions are out there. edgeR vignette even contains a section about it.

ADD REPLY • link 4.5 years ago by ATpoint 81k

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Anybody has any suggestion on how to proceed with DEG without replicates.

You don't do deg without replicates.

ADD REPLY • link 4.5 years ago by WouterDeCoster 47k

score 2 · Answer 1 · 2019-10-11

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4.5 years ago

swbarnes2 14k

I'd use something like DESeq2 or edgeR for size normalization only, compare normalized counts in Excel, and tell the people who designed this that your conclusions are very poorly supported because the experimental design is terrible; that if they want to do this right, they need replicates.

ADD COMMENT • link 4.5 years ago by swbarnes2 14k