I ran ANCOM on my data. I used all the filters that are recommended. I removed features that only appear in 1 sample and removed features whose overall frequency was less than 20. In my output (attachment), I see a lot of taxa with high W values but still tagged "FALSE" for the null hypothesis. Can someone help me understand what this means? Thanks a lot. Here is a snapshot from my results
ancom (4).tsv (11.7 KB)
Hi. Did anyone notice high W values, but still coming out as "FALSE" under the Reject Null Hypothesis column. Attaching a result that shows HIGH W values but only one "ancom (4).tsv (11.7 KB) TRUE"
How many features are in your table prior to ANCOM testing and how many samples do you have?
Thank you for responding. I am comparing two groups (T_Control and cB_Control) of samples (each having 5 samples each). I am also attaching my script that I used for the same.
ANCOM_script.txt (1.3 KB)
My overall feature table has 728 features but I used filters
- First to filter out samples with less than 22000 reads,
- Remove features that only appear in 2 samples
- Remove features whose overall frequency is less than 20.
I then collapse the filtered table to a genus level data.
I suspect the answer is more aggressive filtering.
How many genera do you have? What portion of the genera is 109? I’m guessing it’s 50% or fewer?
That is what baffled me as well. The total number of genera in my collapsed file are only 114. I have attached it for you to see.collapsed_table.tsv (22.5 KB)
Thanks for being patient with me, I’m going in circles a little bit. The file you sent gives a significant signal at W=109 (0.95), but not at W=96 (0.84) with a total of 10 samples. ANCOM tends to be quite conservative so the fact that you’re geting a signal at all wtih 10 samples impresses me.
The way the “significant” results are calculated in ANCOM I uses a bimodal approximation of a null distribution and essentially fits the data to estimate that null. So, I think the results make sense to me here.
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