Question: 2x2 design - UP means more expression on S than R and DOWN less expression on S than R?
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gravatar for filipematias23
10 months ago by
filipematias230 wrote:

Hi everyone,

Could you guys help me to understand my deseq2 outputs?

I used the coding 2x2 design to compare a resistant (R) and susceptible (S) plants. In this intention, we used two biological replicates for susceptible (RED – treatment, and YELLOW – control) and three replicates of resistant (GREEN – treatment and BLUE – control). I would like to know, how the controls are being used? Is the test correct the counts of treatments by control first and then compare R and S? Are the results below showing that UP means more expression on S than R and DOWN less expression on S than R?

Thank you,

Matias

deseq2 2x2 • 125 views
ADD COMMENTlink modified 10 months ago by Michael Love22k • written 10 months ago by filipematias230

Please post your code, including the design, and the colData so we can have a better idea of what you are doing.

http://www.bioconductor.org/help/support/posting-guide/

ADD REPLYlink written 10 months ago by Michael Love22k
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