DESeq2 paramter inference
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BioEpi • 0
@11b02720
Last seen 3 days ago
United States

Hello Mike, I have one question about the DESeq2 model. Given that I have 2 groups of RNA-seq, each of which has 3 biological replicates. Thus, each gene has 3 biological replicates in each condiction. does the DESeq2 model use average gene expression or each replicate of gene to estimate paratmeters, such as beta and intercept? Thanks

DESeq2 • 81 views
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@mikelove
Last seen 1 day ago
United States

This is described best in the DESeq2 paper, it's a GLM. It does not just use the average, but uses each sample and takes into account the depth for each sample (and optionally other factors such as technical biases if a method such as tximport is used).

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Hello Michael, thanks for your reply. Yes, I know that DESeq2 normalizes each gene in each sample. after normalization, we will have normalized expression level for each gene in each sample.

here is an example: enter image description here

enter image description here My question is: how does y(DESeq2) take in these normalized gene expression to build GLM? does DESeq2 use average normalized expression of each gene in each group or just use normalized expression of each gene in each group?

I am not sure whether my question is clear.

Best,

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