Identifying unique DEG and synergistically affected genes in a combination treatment (DESeq2)
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mattobu83 • 0
@mattobu83-21662
Last seen 4.6 years ago

Hi,

For my experiment, I treated one group of cells with drug A, another group with drug B, and another group with a combination of both. The last group I did not treat. For each of the 4 conditions (untreated, A only, B only, A+B), I have three biological replicates, for a total of 12 samples. I would like to identify genes that are synergistically affected in the combination condition in addition to the genes that are uniquely differentially expressed in the combination condition. In order to do so, I created a colData table:

Sample                A                  B
K1-3(UT)              UT                 UT

K4-6(A)               T                  UT

K7-9(B)               UT                 T

K10-12(A+B)           T                  T

With this colData table, my design is as follows: ~A + B + A:B. Is this the correct design and colData? How do I set the retrieve the genes I want? I suspect I can use a likelihood ratio test with a reduced formula of ~A+B but I’m not sure how to retrieve the features of interest after applying the test. Please help!

deseq2 • 241 views
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@mikelove
Last seen 1 hour ago
United States

Please read the vignette section on interactions first. You can also look up ?results for more help on how the function works.

The support site is really more for software related questions. If you have questions about statistical models and how interaction terms work, you might first consult some online material, textbooks or consult with a statistician.

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