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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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MicrobiomeSeq not working on phyloseq object #1268

Open samd1993 opened 5 years ago

samd1993 commented 5 years ago

Hi all,

I am having a lot of issues with MicrobiomeSeq. Here are some example of errors I am getting:

kw_sig <- kruskal_abundance(SL5, grouping_column = DS5var) Error in kruskal.test.default(data[, i], g = meta_table$Groups) : 'x' and 'g' must have the same length

or

deseq_sig <- differential_abundance(PS5, grouping_column = "Variable", output_norm = "log-relative", pvalue.threshold = 0.05, lfc.threshold = 0, filename = results) Error in terms.formula(formula, data = data) : '.' in formula and no 'data' argument

Curious if anyone else had similar issues?

DrMaestre commented 3 years ago

Same here

aarti-r commented 1 year ago

Did you manage to solve this issue?

samd1993 commented 1 year ago

nope but I am now using the DESeq2 pacakge in R on its own and it has been working fine for me

aarti-r commented 1 year ago

nope but I am now using the DESeq2 pacakge in R on its own and it has been working fine for me

okay, thank you