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Old 12-13-2013, 11:58 PM   #1
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Location: USA

Join Date: Feb 2012
Posts: 7
Default DESeq2: diff gene expression between species using gene-specific normalization factor


I'm trying to do differential gene expression analysis between the orthologous genes of two species. Leaving aside the technical and biological complications that this kind of analysis carries, I would like to use DESeq2 to perform the computations.

To do so, I'm thinking in take advantage of the gene-specific normalization factors (NF_i,j) of DESeq2, which are used, alongside the common scale quantity q_i,j, to define the expected value of observed counts in gene i and sample j (mu_i,j):

mu_i,j = q_i,j * NF_i,j

Since in my case besides differences in the library size between samples, I also have to take care of the differences in gene length between species, I'm using a form of NF_i,j defined as:

NF_i,j = s_j * L_i,j

Where L_i,j is the length of gene i on condition j, and s_j has the same meaning that in regular analysis but is computed using length-normalized counts:

s_j = median_i { ( k_i,j / L_i,j ) / [ Prod_{v=1,...,m} k_i,v / L_i,j ]^(1/m) }

I would greatly appreciate any comments on the soundness (or lack of it) of this approach. Better ideas to do the analysis are more than welcome.


Last edited by mra; 12-14-2013 at 11:30 AM.
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