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ggloor / ALDEx_bioc

ALDEx_bioc is the working directory for updating bioconductor
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Subsetting / pairwise comparisons #46

Closed elayton13 closed 2 years ago

elayton13 commented 2 years ago

Hello

I am looking to use ALDEx to analyse my picrust data. I have the map files and the picrust output file for all of my samples. Am I right in thinking that in order to do pairwise comparisons I just subset the columns of my picrust output (attached as p2EC) to only include the two groups that I am interested in, and then create a vector called conds as in the vignette:

conds <- c(rep("NS", 7), rep("S", 7)) x.all <- aldex(selex.sub, conds, mc.samples=16, test="t", effect=TRUE, include.sample.summary=FALSE, denom="all", verbose=FALSE)

And that the conds need to be listed in the order of the columns in the picrust data file to enable pairwise comparison? Just wanted to also double check that there is no other pre-processing required of the picrust output data file.

Thank you run1_EC_data.tsv.gz

ggloor commented 2 years ago

yes, if your data is (c1,e1,c2,e2 ... ) or (c1,c2,...,e1,e2...) then pairwise analysis should work.