How to test abundance difference

[Dandydane]

Library phyoloseq Data= Globalpatterns
GP = filter_taxa(GlobalPatterns, function(x) sum(x > 3) > (0.2*length(x)), TRUE)
Define a human versus non-human categorical variable, and add this new variable to sample data:
sample_data(GP)$human = factor( get_variable(GP, "SampleType") %in% c("Feces", "Mock", "Skin", "Tongue") )
Standardize abundances to the median sequencing depth

total = median(sample_sums(GP))
standf = function(x, t=total) round(t * (x / sum(x)))
gps = transform_sample_counts(GP, standf)

Filter the taxa using a cutoff of 3.0 for the Coefficient of Variation

gpsf = filter_taxa(gps, function(x) sd(x)/mean(x) > 3.0, TRUE)
Subset the data to Bacteroidetes, used in some plots
gpsfb = subset_taxa(gpsf, Phylum=="Bacteroidetes")Plotting the the data

title = "plot_bar; Bacteroidetes-only"
plot_bar(gpsfb, "SampleType", "Abundance", title=title)

Question: What code do i need to write, to test difference in abundance of Bacteroidetes for specific sampletype like feces with ect ANOVA with current example?

[MSMortensen]

If you are looking for differential abundance of all OTUs, I recommend that you try using the DAtest (github.com/Russel88/DAtest). It is easy to use and has a very thorough description.
The package is published on BiorXciv, but I don't have the link...

Regards,
Martin

[spholmes]

Following the standard differential abundance methods inspired from RNA-seq studies, you can use DESeq2 see the tutorial here: http://joey711.github.io/phyloseq-extensions/DESeq2.html

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On Sun, Jun 3, 2018 at 11:54 AM, Dandydane ***@***.***> wrote: Library phyoloseq Data= Globalpatterns GP = filter_taxa(GlobalPatterns, function(x) sum(x > 3) > (0.2*length(x)), TRUE) Define a human versus non-human categorical variable, and add this new variable to sample data: sample_data(GP)$human = factor( get_variable(GP, "SampleType") %in% c("Feces", "Mock", "Skin", "Tongue") ) Standardize abundances to the median sequencing depth total = median(sample_sums(GP)) standf = function(x, t=total) round(t * (x / sum(x))) gps = transform_sample_counts(GP, standf) Filter the taxa using a cutoff of 3.0 for the Coefficient of Variation gpsf = filter_taxa(gps, function(x) sd(x)/mean(x) > 3.0, TRUE) Subset the data to Bacteroidetes, used in some plots gpsfb = subset_taxa(gpsf, Phylum=="Bacteroidetes")Plotting the the data title = "plot_bar; Bacteroidetes-only" plot_bar(gpsfb, "SampleType", "Abundance", title=title) Question: What code do i need to write, to test difference in abundance of Bacteroidetes for specific sampletype like feces with ect ANOVA with current example? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#951>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABJcvfFMG4jHWbW6ewWGQ0RzHepQWjnUks5t5DD5gaJpZM4UYMZf> .

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