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umerijaz / microbiomeSeq

An R package for microbial community analysis in an environmental context
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Error in correlation between taxa abundance and environmental variables in microbiomeseq #27

Open smmontanos opened 5 years ago

smmontanos commented 5 years ago

The package Microbiomeseq in R helps me a lot, however, I have an issue when I tried to run taxa.env.correlation, with this code in R:

`phyfa <- taxa_level(physeq, "Family")

env.taxa.cor <- taxa.env.correlation(phyfa, grouping_column = "Specie", method = "pearson", pvalue.threshold = 0.05, padjust.method = "BH", adjustment = 5, num.taxa = 10, select.variables = NULL)`

Error in cor.test.default(a[complete.cases(b), ], b[complete.cases(b), : not enough finite observations

I don´t know what is the problem, because I update all necessary packages for microbiomeseq, and I have phyloseq object correctly. Any suggestions and help to do this analysis plotting the results???

AlfredUg commented 5 years ago

Hey @smmontanos, The issue has been fixed, re-install microbiomeSeq and re-run your analysis. It should work fine, let us know if it doesn't.

smmontanos commented 5 years ago

Hello @AlfredUg ,

I don´t know what happend, but the error still in my code !!!

aimeelmassey commented 4 years ago

I am having this same issue - my phyloseq object works with other functions but not taxa.env.correlation. My OTU abundance matrix has some NA's but I have tried including samples and OTU's with the least amount of NA's and I still receive this error.

carloshenriquezc commented 3 years ago

Hello,

Thanks for sharing your routine,

I still having the same issue:

Error in cor.test.default(a[complete.cases(b), ], b[complete.cases(b), : not enough finite observations

Catastrofix commented 3 years ago

I am having the same issue, is there a way to solve this problem?

NataliHB commented 3 years ago

I have the same issue, Does anyone now how to fix it?