Question: DESeq2 likelihood ratio test log fold change interpretation/calculation
gravatar for Argonaut
7 weeks ago by
Argonaut0 wrote:


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

##### dds <- DESeqDataSetFromMatrix(countData = data, colData = meta, design = ~ genotype)
### 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.

lrt rna-seq deseq2 • 158 views
ADD COMMENTlink modified 7 weeks ago by Kevin Blighe61k • written 7 weeks ago by Argonaut0
gravatar for Kevin Blighe
7 weeks ago by
Kevin Blighe61k
University College London
Kevin Blighe61k wrote:

Correct, the p-value is derived from the deviance between the groups.

The fold-change that is output is for just one of the pairwise comparisons. If you want another fold-change, then use the name parameter when calling results.


ADD COMMENTlink written 7 weeks ago by Kevin Blighe61k
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