Hey guys, I wanted to know if ANCOM-BC inside qiime2 corrects for covariable effect the same way as ANCOM-BC 2 (performed in R) does. I'm asking this because I have run ANCOM-BC for a dataset in which, considering q-value < 0.2, only two taxa resulted in the output. In the same pace as performing A…

Hi again, I've never used ANCOM-BC for numerical columns, only categorical, so take my words with a grain of salt. Regarding the first error, this is the (most) interesting part: [image] Liviacmg: Error in relevel.factor(md[[column]], ref = intercept_vector) : 'ref' must be an existing level C…

Hi @Liviacmg , Just wanted to jump in here with a few additional details. The ANCOM-BC method that lives in q2-composition is a wrapper around the ANCOM-BC R package - which is not the same type of model as ANCOM-BC2. ANCOM-BC is a gaussian mixture model and only handles fixed effects, and ANCOM-BC2…

Hi @lizgehret , Thank you so much for your insightful response! Also, I was checking the inputs for both ANCOM-BC and ANCOM-BC2 and in the first one I used qiime taxa collapse (which is also recommended in qiime2 tutorials, in order to look into the genus level), which led me to think that maybe t…

Hi @lizgehret , Sorry for having another question haha But do you know if in ANCOM-BC the correction for the covariates is carried out only on the significant taxa after the FDR correction, or on all the taxa present in the database (OTU table)? Thank you in advance.

Hi @Liviacmg - I found this paper (see below) and a direct quote from it stating that it is for each taxa. I’ve emboldened it in the excerpt below. I hope it helps! Reference: Lin, H., & Peddada, S. D. (2020). Analysis of compositions of microbiomes with bias correction. Nature Communications, 11,…

Hi @Liviacmg , @Mike_Stevenson is correct with regards to his answer to your second question! [image] Liviacmg: I was checking the inputs for both ANCOM-BC and ANCOM-BC2 and in the first one I used qiime taxa collapse (which is also recommended in qiime2 tutorials, in order to look into the gen…

Hi @Mike_Stevenson , Thank you so much!! :slight_smile:

Hi @lizgehret , Thank you again!! :slight_smile:

Hi @lizgehret and @Mike_Stevenson , I know ANCOM-BC 2 is still not implemented in qiime2 but do you happen to know in relation to which group this graphic from ANCOM-BC 2 is plotted? For example, in the following image from the tutorial ( ANCOM-BC2 Tutorial ): [image] It does not say in relation t…

Hey @Liviacmg , That's a great question! The intercept or reference shown in this plot (and what all the LFC groups are with respect to in ANCOM-BC/BC2 results) will be the first ordered level. So if you didn't specify the level ordering, it would default to the first group in alphabetical order (ju…

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Does ANCOM-BC on qiime2 corrects for covariates?

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