Accounting for fish body mass in DE?
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@e2642572
Last seen 8 months ago

Hi,

I'm currently using EdgeR to look at DE in fishes in response to a toxicant and a control. I'm using a pairwise approach looking at control-treatment comparisons within 3 time points (e.g. C vs T @ 12 h, C vs T @ 24 h, etc). I'm noticing some potential effects of body mass on driving some of the relationships in driving the gene responses and wanted to include each individual's mass as a factor in the model. However, I've been trying to find documentation on the proper way to set this up in the model and have been unable to locate anything. I was wondering if anyone could point me in the right direction for previous examples. I was thinking it may be a similar setup to the batch effect example provided in the user's guide but am unsure.

Thank you for your time and any help you could provide would be greatly appreciated!

Edit: I currently have my model matrix setup as the following testing for treatment/time effects:


design <- model.matrix(~0 + Nic_Gill_edgeR$samples$group)
GeneExpression edgeR • 250 views
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@james-w-macdonald-5106
Last seen 1 day ago
United States

Not knowing what is in Nic_Gill_edgeR$samples$group, that particular detail isn't particularly helpful.

Anyway, assuming that your group is basically a combination of time and treatment, and you are using a contrast matrix to make comparisons, you can simply add another column to your design matrix containing the body mass of the fish. You will then need to add a row of zeros to your contrast matrix (or simply use makeContrasts, which will handle the details for you).

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