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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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differential_abundance.py mapping file subcategory/group order in output file #2154

Closed borax closed 8 years ago

borax commented 8 years ago

I am using the differential_abundance.py tool to test for taxa abundance differences between sample categories, with the metagenomeSeq algorithm. It's great! However, there doesn't seem to be a connection between the subgroups in my mapping file I pass after -x and -y and which of the two subgroups get considered "group 0" and "group 1" in the output file (for the "+samples in group" and "counts in group" columns). As far as I can tell group 0 vs. 1 is determined by alphabetical/numerical order of the subcategory name? It would be very nice if there was consistency in the output connected to -x and -y, or if what to expect was stated in the documentation somewhere, because the actual subcategory names I include in the command aren't included anywhere in the output file to make a connection with groups 0 and 1. If I missed where it was stated, I apologize. I would just like to be able to easily tell in which subcategory a taxa is enriched.

Thanks!

gregcaporaso commented 8 years ago

Hi @borax, Could you please post your question to the QIIME Forum? It helps us to consolidate these types of support questions there. Thanks!