gravatar for Argonaut

2 hours ago by

Hi,

I am using DESeq2 Likelihood Ratio Test for multi-group comparison (6 different genotypes).

Example

<h5>dds <- DESeqDataSetFromMatrix(countData = data, colData = meta, design = ~ genotype)</h5>

Likelihood ratio test

dds_lrt <- DESeq(dds, test="LRT", reduced = ~ 1)

As far as I know LRT doesn't use log2foldchange to calculate the p.value. Thus, I am interested to know how DESeq2 calculates these fold changes ( 6 genotypes in my case), and is there any way to interpret them.

Thanks!
PS. I would appreciate any link to the tutorial/paper on how to perform multi-group RNA-seq analysis and interpret it.



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