I am using the multivariate analysis feature to perform pairwise comparisons among levels within different factors in my data set. Specifically, within the factor “Exposure_group”, I want to compare 1 day vs 3 days, 3 days vs 7 days, and 7 days vs 1 day. I control for the factor “Response_time”. And I’m comparing at the family level. And I’m using the lm model.
I’ve successfully run this test on a lot of other pairwise comparisons (and previously for prior papers), but noticed a problem recently with different pairwise tests giving the same resulting p-values. And, when trying to repeat a comparison, I sometimes get different results or even no results (no significant features found). And, when repeating a comparison forwards (e.g., 1 day vs 3 days repeated in reverse as 3 days vs 1 day), getting different results and log2FC values that are not matching up in value or opposite direction (+2 should be -2 if flipped). Sometimes I get the same exact data (the log2 FC, raw p-val and adj p-val) for different comparisons, which is just impossible. I have re-uploaded the data and tried bunches of times. I’m just not sure now what to trust. I wonder if something is just not “resetting” with the commands for the pairwise tests when the comparison is changed?
Here are a couple of the data files I’m working with. These are subsets of data for different levels of the main factor Supplement.
BB.txt (500.6 KB)
BC.txt (486.3 KB)
BRB.txt (491.2 KB)
CON.txt (499.6 KB)
And here is the metadata file, which has all the metadata for all levels of Supplement and can be used for any of the count files above.
ProjO_Metadata_cleaned.txt (92.8 KB)
And, then the taxonomy and tree file
Taxonomy.txt (274.0 KB)
rooted-tree.txt (134.7 KB)
(I had to change the file from .nwk to .txt to get it to upload. You may want to change it back)
These are mapped to Silva.
I hope we can get this sorted ASAP, as my student is up against a dissertation deadline. We didn’t anticipate having this kind of problem when finalizing his data analysis.
Thanks,
Abby Benninghoff
Utah State University
abby.benninghoff@usu.edu