Thanks a lot @fbeghini. I am following the tutorial and successfully imported it in phyloseq.
But I am facing one important “ERROR” there which says the abundance proportion is not accepted their. They accepts read count. Have you ever tried phyloseq and encountered such error? Do you have any other way to do the analysis within phyloseq bypassing this problem? Here is the error message:
alpha_meas = c(“Observed”, “Chao1”, “ACE”, “Shannon”, “Simpson”, “InvSimpson”)
p <- plot_richness(physeq1, “type”, measures=alpha_meas, color=“time”)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 't': function accepts only integers (counts)
In addition: Warning message:
In estimate_richness(physeq, split = TRUE, measures = measures) :
The data you have provided does not have
any singletons. This is highly suspicious. Results of richness
estimates (for example) are probably unreliable, or wrong, if you have already
trimmed low-abundance taxa from the data.
We recommended that you find the un-trimmed data and retry.
Thanks and regards,