Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Improbably huge log-fold change values #293

Open
LLansing opened this issue Oct 31, 2024 · 0 comments
Open

Improbably huge log-fold change values #293

LLansing opened this issue Oct 31, 2024 · 0 comments

Comments

@LLansing
Copy link

In an ANCOM-BC2 output (res_pair table), a few of my taxa have improbably huge lfc values (-146 and -4696). In many of my samples the taxon has a 0 abundance, but there are still enough samples with non-zero values to pass the default prv_cut of 0.1.

By plotting the bias-corrected log abundances (image) and/or the raw abundances of these taxa across my group variable as box plots, I can see that the distributions don't seem to support such huge lfc values.

image

3/4 of the results with huge lfc also have significant adjusted p-values AND passed the pseudo-sensitivity test (diff & passed.ss):
image

What could be the source of my analysis producing these values? Does it have to do with low-numbers of non-zero samples within the groups? For reference, I have ~150 samples in this example and thus only a fairly small proportion have non-zero values, as shown by the grey dots on the box plots.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant