trans_norm adding a new method?

[marwa38]

Hi Chi SRS is a method of normalization that is being used instead of rarefaction (which got huge debate against). Any possibility to add as an option? it also produces a curve as rarefaction "Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is the current standard method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, researchers explicitly advised against the use of rarefying. Here we introduce a normalization method for species count data called scaling with ranked subsampling (SRS) and demonstrate its suitability for the analysis of microbial communities." from https://peerj.com/articles/9593/ It also has the shinyGo option: scripts Thanks Marwa

[ChiLiubio]

Thanks. The SRS method has been implemented in the rarefy_samples function of microtable class.

# first install SRS package
install.packages("SRS")
# example
library(microeco)
data(sample_info_16S)
data(otu_table_16S)
d1 <- microtable$new(sample_table = sample_info_16S, otu_table = otu_table_16S)
# rarefaction; default method
d2 <- clone(d1)
d2$rarefy_samples(sample.size = 10000)
View(d2$otu_table)
# SRS when method = "SRS"
d3 <- clone(d1)
d3$rarefy_samples(method = "SRS", sample.size = 10000)
View(d3$otu_table)
d3$sample_sums()

[ChiLiubio]

Sorry. A minor bug about feature names reassignment is found. I have fixed it in github.

[marwa38]

Many thanks, Chi, it worked fine. I tried to plot a rarefaction curve using the following from the tutorial but it didn't work and it give an error (below). t1$plot_rarefy(color_values = rep("grey", 100), show_point = TRUE, add_fitting = FALSE, show_legend = FALSE)

[ChiLiubio]

The plot_rarefy is in trans_rarefy class of mecodev package (https://chiliubio.github.io/microeco_tutorial/mecodev-package.html#trans_rarefy), not microtable class. Please check your steps.

[marwa38]

Any possibility to transform a microtable to phyloseq object? I know that the other option is available from phyloseq to microtable. I am running some downstream analysis that I already have workflow for (ggplots for alpha diversity), but just need to run on the SRS output of microtable. Any help with that, please? I have been trying several things since three days, nothing seems to work.

[ChiLiubio]

Please try to use meco2phyloseq function of file2meco package (https://chiliubio.github.io/microeco_tutorial/file2meco-package.html#phyloseq).

[marwa38]

Thank you so much, Chi.

[wangcxv]

@ChiLiubio Hi Chi, I am using the v1.5.0, but an error showed "Error in meco2phyloseq(dataset) : could not find function "meco2phyloseq"", I can not fix it, could you tell me how to deal with it? P.s. : similar errors as "Error: object 'trans_norm' not found". Thanks!

[milyzhou]

Hi chi, I want to use 'trans_norm' normalize data, a similar error as "Error: object 'trans_norm' not found". Can you check the function is working correctly? Thanks. I am using the v1.6.0v

[ChiLiubio]

Hi. Please use ?trans_norm to find the document.

[milyzhou]

[ChiLiubio]

Hi. trans_norm class is now in microeco package, not the mecodev. https://chiliubio.github.io/microeco_tutorial/other-examples-1.html#trans_norm