Issues with running Gneiss, loading regression summary, and Firefox - view.qiime2.org compatibility

[Nicholas_Bokulich]

Hi @Alex_14262,

@Alex_14262

I wanted to ask how would one choose a sensible value for filtering?

I am not sure there are really solid guidelines that would cover all cases; it will largely depend on a user's own expectations about their data, and overall sequencing depth. As @mortonjt indicated in this post:

@mortonjt

The filtering recommendations are done based on empirical evidence. We have seen wonky behavior when there is a lot of low abundance features. It would be great to have insights from the original authors on this though. In addition, ANCOM is very slow when the number of features is high, since it scales quadratically with the number of features, so filtering definitely helps with runtime.

But a min-frequency of 10 seems reasonable to me as a threshold for cutting off low-abundance features.

@Alex_14262

I have been having issues with visualizing the regression summary.qzv in qiime view. The tables load quite quickly, but the figures don’t. I keep getting the message: “A web page is slowing down your browser. What would you like to do? Stop it/Wait”

Sounds like either:

1. this is a memory error, due to constrained memory inside the virtual box (and/or a very large QZV). Toss the file in the shared folder and view outside — does this fix things?
2. there is an issue with firefox (is it the latest version? is this compatible?)

I hope that helps!