Normalized counts bulk RNA-seq to DEGs
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13 months ago
t.ru ▴ 20

Hi,

I have a RNA-seq count matrix and normalized by DESeq2. Unfortunately, I need to improve a workflow to find DEGs from the normalized count. I already checked edgeR, DESeq2 and limma. However, they required un-normalized count matrix. Do you have any suggestion? Thanks.

RNA-seq • 1.1k views
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I do not understand your question, you said you started with a count matrix that you normalized with DESeq2. Why don't you follow the DESeq2 workflow until the end ?

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I only have output as normalized counts. I did not do that part.

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Then ask for raw counts. Analysis is anyway not reproducible and hence not publishable without the raw data at hand.

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Follow up on DESeq2 for different design and normalized counts and your many previous questions from which many received no upvotes or accepts.

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13 months ago
LauferVA 4.3k

You need to go to the source manuscript and obtain raw data. What is the dataset you are trying to analyze

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