Question: Focused gene set tests
gravatar for SB
5 months ago by
United States
SB0 wrote:

Dear Bioconductor community,

I'm looking for gene set analysis tests that produce a quantitative value for each set and sample/comparison along with a p-value and are designed (or at least have proven to perform well) for focused gene set testing with 2 custom gene sets. Further, I'm looking for tests that work with datasets composed of several sample groups with only a few replicates per sample group. So far it seems like ROAST, CAMERA, SAM-GS, and GlobalTest might work well for my study. Any suggestions regarding these tests or other tests that might work would be appeciated.



ADD COMMENTlink modified 7 weeks ago • written 5 months ago by SB0
Answer: Focused gene set tests
gravatar for Gordon Smyth
5 months ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

In the ROAST paper (Wu et al, 2010) we tested ROAST on very highly right skew data (exponentially distributed) to assess its robustness and found it still performed well. It's hard to imagine how you could get such right skew values from real data however.

Three Months Later

If my answer seems a strange response to the question, that's because OP rewrote the question 3 months after originally asking it. The original question said

"Further, I'm looking for a test that works with data that is highly right skewed (and can't be transformed to a log-normal distribution) and has 12-30 samples (3-4 replicates per sample group)."

ADD COMMENTlink modified 6 weeks ago • written 5 months ago by Gordon Smyth37k
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