Closed sbslee closed 3 years ago
The aldex.ttest functions as you described it above. It uses the order of samples to set up the pairing relationships.
The aldex.ttest returns the expected value across the MC samples of the corresponding tests in multtest:mt.teststat. So the tests are returning what you indicated, except they are average values
@ggloor, thank you for answering my questions! It totally makes sense. Closing this issue.
Hello @ggloor,
This is just a quick follow-up to the recently closed issue #33 where you mentioned:
I'm just trying to see if I fully understand how to use the
aldex.ttest
function in the context of paired testing.For this, let us use the example given for the
aldex.ttest
function in the manual as shown below.Note that this example does NOT use paired testing. But let's keep going...
Here, the
selex
dataframe contains 14 samples and 400 features. The samples have a condition of either "NS" or "S".Now, we can see which features were determined to be significantly differentially abundant by ALDEx2:
So far so good. But now, imagine I want to perform paired testing with this dataset. For that, I can do the following:
Basically, above is comparing the samples in the following way:
And now my questions:
Q1. Could you kindly confirm my understanding of the `aldex.ttest' function for paired testing is correct (as described above)?
Q2. Could you confirm
aldex.ttest(x, paired.test=TRUE)
will output results of paired Welch’s t-test (i.e.we.ep
) and Wilcoxon signed-rank test (i.e.wi.ep
)?Thank you very much for reading this. I'm very excited to try out the
aldex.ttest
function for my own dataset (microbiome data from normal tissue vs. tumor tissue from cancer patients).