Question: 2x2 design - UP means more expression on S than R and DOWN less expression on S than R?
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filipematias23 • 0 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
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modified 17 months ago
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Michael Love ♦ 26k
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17 months ago by
filipematias23 • 0


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/