Dear all,
I have a dataset consisting of a matrix of gene counts for two different conditions with 3 biological replicates each and I want to call diff-expressed genes in response to the treatment.
However, I am wondering which parameters are most appropriate for me to use in the estimateDispersions function:
1. method: per-condition or pooled
2. fitType: parametric, local
1. I don't exactly understand which difference both functions have computationally; in general per-condition seems more logical to me. I have calculated the amount of diffex genes with both methods and contrary to my expectation the per-condition parameter resulted in more sig. diffex genes.
Can anyone give me some advise on what to choose and WHY it might be more realistic?
2. Here I also don't know which setting makes more sense and why. I'd be thankful for suggestions!
Thanks a lot!
I have a dataset consisting of a matrix of gene counts for two different conditions with 3 biological replicates each and I want to call diff-expressed genes in response to the treatment.
However, I am wondering which parameters are most appropriate for me to use in the estimateDispersions function:
1. method: per-condition or pooled
2. fitType: parametric, local
1. I don't exactly understand which difference both functions have computationally; in general per-condition seems more logical to me. I have calculated the amount of diffex genes with both methods and contrary to my expectation the per-condition parameter resulted in more sig. diffex genes.
Can anyone give me some advise on what to choose and WHY it might be more realistic?
2. Here I also don't know which setting makes more sense and why. I'd be thankful for suggestions!
Thanks a lot!
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