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Questions when using it in bulk RNA-seq #13

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OdysseyXD opened this issue Mar 23, 2024 · 1 comment
Open

Questions when using it in bulk RNA-seq #13

OdysseyXD opened this issue Mar 23, 2024 · 1 comment

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@OdysseyXD
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OdysseyXD commented Mar 23, 2024 •
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Hi!
I'm not very familar with GRN, I got some questions after reading GENIE3 vignette.

  1. Is that sample number matters? What's a proper sample number?
  2. Is the treat method of sample matters? Like "treat" group and "control" group.
@OdysseyXD OdysseyXD changed the title Questions when using it in RNA-seq Questions when using it in bulk RNA-seq Mar 23, 2024
@vahuynh
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vahuynh commented Mar 27, 2024

Hi,

  1. Regarding the sample size, unfortunately there is no direct answer to that question. This very much depends on the data and on the number of candidate regulators that you have.
  2. It depends on what type of GRN you want to reconstruct. If you include only samples related to the treatment group, GENIE3 will learn the GRN that is specific to that treatment. If you include both treatment and control samples, it will learn a GRN that is rather a consensus between the two groups.

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@vahuynh @OdysseyXD