I have to perform ANOVA test on my samples. I would like to know to analyse in qiime2. What are the commands and and how one can choose value for --p-formula.
Please see following Docstring in qiim2 tutorial.
Usage: qiime longitudinal anova [OPTIONS]
Perform an ANOVA test on any factors present in a metadata file and/or
metadata-transformable artifacts. This is followed by pairwise t-tests to
examine pairwise differences between categorical sample groups.
(multiple Sample metadata containing formula terms.
be merged) [required]
–p-formula TEXT R-style formula specifying the model. All terms must
be present in the sample metadata or
metadata-transformable artifacts and can be continuous
or categorical metadata columns. Formulae will be in
the format “a ~ b + c”, where “a” is the metric
(dependent variable) and “b” and “c” are independent
covariates. Use “+” to add a variable; “+ a:b” to add
an interaction between variables a and b; “*” to
include a variable and all interactions; and “-” to
subtract a particular term (e.g., an interaction term).
for full documentation of valid formula operators.
Always enclose formulae in quotes to avoid unpleasant
–p-sstype TEXT Choices(‘I’, ‘II’, ‘III’)
Type of sum of squares calculation to perform (I, II,
or III). [default: ‘II’]
How to construct above formula using R-style formula specifying the model. .
This error is a little cryptic. Before we get into the statistical test and what ‘asymptotically non-normal’ means, let’s take a look at the formula.
Your formula is faith_pd ~ SampleNumber+Area
You could say, “How is faith_pd affected by changes in SampleNumber and Area?”
So… let’s take a look at your SampleNumber and Area categories:
SampleNumber: 7 different levels (all levels are different)
Area: 1 level (all levels are the same)
“How do changes in Area effect faith_pd?” We don’t know because Area never changes.
“How do changes in SampleNumber effect faith_pd?” SampleNumber is always changing, so I guess faith_pd is always changing too!
Take a look at this metadata table from a small project:
Based on this table, we could ask “How do changes in Treatment and Time effect faith_pd” and write this formula: faith_pd ~ Treatment+WeeksAfterInfection
Because our values are not all the same or all different, we can answer this question.
Which metadata categories would you like to test with your samples?