I am using QIIME2 for the statistical analysis of my study data using gneiss. I have three questions.
- I used QIIME 1.8 (UCLUST- open-reference OTU picking) with gg13_5 to get my BIOM file. Which taxonomy file I will use in the “qiime gneiss balance-taxonomy” command to specify
--i-taxonomy? Or how can I generate a taxonomy file from the BIOM file for gneiss?
- How can I get a beta and standard error for individual bacterial taxa those are explaining the differences between the treatment and control groups?
- Can gneiss take and analyze interactions (e.g., sex X treatment groups) in the regression model?
Thank you so much for developing QIIME2 and Gneiss.
Hi @nhuda6! We are pinging @mortonjt for some assistance with your questions - he is the brains behind
gneiss. Stay tuned!
@thermokarst, thank you so much. I am waiting for reply from @mortonjt.
Thank you so much for your reply. I am happy that we can now analyze interactions effects with microbiota data. Thank you so much for the beta and residuals. However, I have few follow-up questions.
- We already had analyzed our microbiota data by QIIME 1.8 (as indicated in the earlier post). We want to keep consistency and do not want to reanalyze them by QIIME2 (at least for now). Is there any way we can create the taxonomy file from the QIIME 1.8 BIOM file? Or do you have any other suggestions on this? I know some other people also have the same issue. I was wondering if @gregcaporaso has any suggestion on this.
- I believe the coefficient (beta) for Subjects (in your tutorial) is adjusted for other confounding factors (Please correct me if I am wrong). My understanding is that the coefficient for a balance, e.g., Y0 (or for a cluster of bacteria). Is there any way we can get coefficient for individual taxa (e.g., a Bacteria genera)? Some researchers will like to see it because it will be easier to interpret.
- Is the coefficient P values FDR adjusted?
- My understanding is that the Residuals are from the overall regression model. How can I get residual for an individual explanatory variable (e.g., Subjects, in your tutorial) adjusted for other confounding factors (e.g., Sex, Age, BMI, sCD14ugml, LBPugml, and LPSpgml)? An easier way to get a standard error would be highly appreciated.
Thank you again for developing Gneiss. I believe it will be a handy tool soon.
Please check out our Importing Tutorial for some general information on importing. Once you have familiarized yourself with those concepts, you can execute an import command similar to what is presented here:
$ qiime tools import \
--input-path my-file.biom \
--output-path my-taxonomy.qza \
--source-format BIOMV210Format \
This will allow you to import
my-file.biom (change this to your file’s name, of course!) as a
FeatureData[Taxonomy] file (you can also name this whatever you want, instead of
Hope that helps!
Thank you so much. I have added 2 pull requests in the GitHub.
Thank you so much for your suggestion. However, I got an error message when I did try to import the “FeatureData[Taxonomy]” from my BIOM file. I used both BIOMV100Format (worked with importing my “FeatureTable[Frequency]”) and BIOMV210Format (did not work for importing my “FeatureTable[Frequency]”). Please see the command and error messages below. I need your suggestion to go forward.
qiime tools import
Exception: No transformation from <class ‘q2_types.feature_table._format.BIOMV100Format’> to <class ‘qiime2.plugin.model.directory_format.TSVTaxonomyDirectoryFormat’>
qiime tools import
ValueError: Failed to sniff InPath(‘w6_even3000_s5_f005p.biom’) as BIOMV210Format. There may be a problem with the sniffer.
Hi @nhuda6! Sorry to hear that things aren’t working for you - it sounds like something is fishy with your BIOM file. Would you be able to share it? Either here, or in a direct message to me, if that works for you. Thanks!
I have found and fixed the issue in my BIOM file. It was probably broken when I converted to hdf5 from json. It is now working. Thanks for the help.
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