BUG: ANCOM-BC Fails if sample IDs look too much like exponent about q2-composition HOT 9 CLOSED

I'm interested in helping with this one.

from q2-composition.

Sounds good @colinbrislawn, what kind of support would you need? Someone on the team in my lab should be able to help out as needed.

from q2-composition.

Proposed change log:

q2-composition

@colinbrislawn and @lizgehret fixed a 🐛 in ANCOM-BC where sample IDs that look like scientific notation (1e23) where being interpreted as numbers.

from q2-composition.

Thanks @colinbrislawn, that would be great. Do you have an idea of timeline? We do have a release coming up around mid-Feb, and it would be nice to get a fix in for this by then (so would probably need a PR by around the end of next week for that to happen).

Let us know if you need any input.

from q2-composition.

If you can provide some support, I bet I can get this submitted by next week.

from q2-composition.

what kind of support would you need?

idk, let's find out!

Chloe, can you send me the forum-table.qza or forum-table-3.txt,
Or maybe just post head forum-table-3.txt here?

I hope this can be fixed with a careful use of read.delim read_csv read_tsv to better support sample names.

from q2-composition.

I've confirmed what Chloe suspected, which is that specific sample names are being converted to numbers.

This only happens when all sample name look like SI notation, e.g. 0001E002
If a single name breaks the format, like L0001E002, it's fine, which is why we haven't see it sooner.

In my testing, simply adding colClasses = c("character") to read.delim() fixes it. I've opened a PR: #131

More testing is needed!

from q2-composition.

Thanks for looking into this. Looks like you made some progress so you might not need it but here is forum-table-2.txt
forum-table-2.txt
This is the file that I got to pass by changing the Es in the sample id column to Fs

from q2-composition.

changelog text looks great, thanks @colinbrislawn! will get this added in the next couple of weeks 🙂

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