Question

Analyzing publicly available DESeq2 normalized counts for differential expression

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krovi138 • 0

@c73520b6

Last seen 4.4 years ago

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Hello all,

I was wondering what the best way would be to analyze data that has already been normalized by the DESeq2 pipeline. There are some datasets that are available on GEO where the available file is an Excel spreadsheet with DESeq2 normalized data. What is the best way to input the data into R and analyze it for me to perform differential expression analysis between the samples?

Thanks so much!

DifferentialExpression DESeq2 Normalization • 1.4k views

ADD COMMENT • link updated 4.4 years ago by Michael Love 43k • written 4.4 years ago by krovi138 • 0

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There are countless threads on what to do with normalized data, please read them. Check the right of this page, there are suggestions in that Similar Posts column. No, DESeq2 won't work as explicitely mentioned in the manual.

ADD REPLY • link 4.4 years ago ATpoint ★ 4.8k

score 1 · Answer 1 · 2020-11-22

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Michael Love 43k

@mikelove

Last seen 8 days ago

United States

See ATpoint comment above (I tried but couldn't mark his comment as answer...)

ADD COMMENT • link 4.4 years ago Michael Love 43k