Closed cherman2 closed 4 months ago
I'm interested in helping with this one.
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.
If you can provide some support, I bet I can get this submitted by next week.
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.
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.
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!
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
Proposed change log:
@colinbrislawn and @lizgehret fixed a :bug: in ANCOM-BC where sample IDs that look like scientific notation (1e23
) where being interpreted as numbers.
changelog text looks great, thanks @colinbrislawn! will get this added in the next couple of weeks 🙂
Bug Description We had a user on the forum that reported getting the error message "duplicate 'row.names' are not allowed " from ANCOM-BC. For this user it was because their sample-ids looked like exponents. My theory is that the sample-ids are losing some resolution when they are converted to exponents and so they are becoming "duplicates". I was able to fix this by replacing sample-ids with E to F and then it worked fine.
Forum x-ref
Steps to reproduce the behavior
Steps to reproduce the solution In python: