Help with multi-factored RNA-seq edgeR model
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cody0071 • 0
Last seen 3.8 years ago

Hello, I am analyzing an experiment and am trying to come up with a model design to compare the differences between 2 treatments and 2 factors. I need help in trying to organize the model design matrix in EdgeR. How can I write the code for them to be recognized? I also need to make sure my replicates are similar to one another in each 'group' in order to effectively compare. I have been analyzing everything separately and then combining results, but I am wondering if there is a more efficient way to go about analyzing the data?

  Factor #1 Factor #2
Treatment #1 4 Replicates 4 Replicates
Treatment #2 4 Replicates 4 Replicates

The table is an overview of the data I have for the RNA-seq experiment. I am interested in any differences between all possibilities. Thanks in advance to any help offered!



edger design model interaction model rnaseq • 431 views
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Last seen 11 hours ago
United States

See section 3.3 of the edgeR User's Guide.


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