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Cannot perform CCA #55

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vfonti opened this issue Jun 29, 2021 · 1 comment
Open

Cannot perform CCA #55

vfonti opened this issue Jun 29, 2021 · 1 comment

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@vfonti
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vfonti commented Jun 29, 2021

Hi everybody,
I hope you can help me with a problem I am facing since a wile. I am tri=ying to perform CCA on my phyloseq object made from 16S amplicon sequencing.

I have staterd with a basic line:
plot_cca(physeq = x, grouping_column = "type")
But I keep having this errore message:
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels

However the "type" grouping variable is a 2 level factor in the sample_data:

`sam_data(indic_families)$type`
 [1] WWTPs    Seawater WWTPs    WWTPs    WWTPs    WWTPs    WWTPs    WWTPs    Seawater
[10] Seawater Seawater Seawater Seawater Seawater WWTPs    WWTPs    WWTPs    WWTPs   
[19] ......
Levels: Seawater WWTPs

I can't figure out what's the problem. My grouping variable is clearly a factor.
I hope somedy can help me...

Cheers

Error in contrasts<-(*tmp*, value = contr.funs[1 + isOF[nn]]) :
contrasts can be applied only to factors with 2 or more levels

@Abonacolta
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I am getting the same error. Any solution yet?

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