Question: How to get fitted per sample means and dispersion from DESeq2?
gravatar for kjkjindal
9 days ago by
kjkjindal0 wrote:


DESeq uses the following model for differential expression analysis:

K_ij ~ NB(mu_ij, alpha_i)

mu_ij = s_j q_ij

log2(q_ij) = x_j. beta_i

Is there a way to access the specific 'mu_ij' and 'alpha_i' values?

I have been looking around and found assays(dds)[['mu']] giving something like mu_ij but am not sure if those are indeed the values that I am looking for.


sequencing rna-seq next-gen R • 75 views
ADD COMMENTlink modified 9 days ago by Kevin Blighe19k • written 9 days ago by kjkjindal0
gravatar for Kevin Blighe
9 days ago by
Kevin Blighe19k
University College London Cancer Institute
Kevin Blighe19k wrote:

Take a look at the Access to all calculated values of the tutorial Analyzing RNA-seq data with DESeq2.

Dispersion is calculated on a gene-wise basis and the final modelled dispersion can be obtained with mcols(dds)$dispersion or dispersions(dds). The estimated gene dispersions that go into the Bayesian model as priors can be obtained with mcols(dds)$dispGeneEst

For the mean, it states:


ADD COMMENTlink written 9 days ago by Kevin Blighe19k

Hi, that worked great. Thanks a lot Kevin!

ADD REPLYlink written 2 days ago by kjkjindal0

You're welcome - no problem.

ADD REPLYlink written 2 days ago by Kevin Blighe19k
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