RNA Seq Analytic Design
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@laurenfitch-11575
Last seen 3.9 years ago

I have RNA seq data from tissues that were treated with several compounds, at different doses. I am analyzing compound vs. vehicle in single comparisons using DESeq2 which is working fine. We are also trying to compare some compounds against each other in the following ways:

(Compound A vs Vehicle 1) vs (Compound B vs Vehicle 1) 

(Compound C vs Vehicle 2) vs (Compound B vs Vehicle 1)

If the vehicle data is the same, can I just directly compare Compound A vs. Compound B? What if it's different? Can I do the 2 comparisons in DESeq2 and then directly take the ratio? That seems overly simple, and I'm not sure how to calculate p-values in that case. Is there a way to write the design formula to accommodate this?

rnaseq deseq2 • 773 views
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@mikelove
Last seen 2 hours ago
United States

See this recent post:

A: How to compute "second-order" differences

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Thank you, this definitely answers my question regarding when the controls are the same. It doesn't seem to apply when the controls are different, though. I edited the original post to make that more clear. Some of my original comparisons have the same denominator and some don't.

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If the comparison is different you can use a numeric contrast. Check resultsNames(dds) to see the coefficients in the model. Then you would give a -1 to a term in the denominator and a +1 to a term in the numerator.

E.g. if the resultsNames are:

Intercept, A, B, C, D

And you want to compare (D vs C) vs (B vs A), this is: (D/C) / (B/A) = AD / BC

So the numeric contrast would be: contrast=c(0,1,-1,-1,1)

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That's helpful, thanks!

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