Significance of PCoA plot using PERM ANOVA

01 January 1970 0 4K Report

Recently, I read an article on AMF succession. In order to explain the dissimilarity in AMF Counts, they have used PCoA plot. Mostly , I have seen the PCoA plot are being constructed by using NMDS or UniFrac, but here they have used PERM ANOVA. Can anyone explain the differences?

Although many discussions have been done on RG regarding PCoA plots but here I want to start discussion mainly on usage of PERM ANOVA.

Badges
Science method

More Rakeshkumar Yadav's questions See All

How do I decide the parameters to run diamond aligner?

My goal is to align my metagenomic sequences with virulence gene database in order to find out which probable genes are prevalent in the data. So I ran diamond aligner using following...

10 November 2019 2,333 2 View

Do i need to do betadispersion after Adonis test?

I am analyzing a meta genomic data and I want to comment about the significance of beta diversity for the samples taken from different locations. In order to do that i did Adonis test (seed of...

07 August 2019 3,969 4 View

Please suggest any bioinformatic tools or lab-based experiments to validate the metagenomic data?

I am looking to validate the information generated from metagenomic sequencing. I know that I can carry out qPCR to validate my data. And I guess Random forest regression analysis can be done too....

03 April 2019 7,128 1 View

Can I convert Nanopore data reads Fast5 or fastq format in to biom format and proceed with the analysis using R ?

Previously, I have done illumina data analysis so have experience in doing that. However, Nanopore is bit new to me and I am quite confused in its data analysis. I have epi2me (I guess it uses...

09 October 2018 7,669 0 View

Wondering how to enrich or concentrate phages or viruses for community phage/virus nucleic acid extraction and that too without using host?

We all know about the specificity of viruses or phages and I guess that would specially limit their enrichment to certain groups. Suppose I have a sediment or sewage sample and I want to enrich...

08 September 2018 6,274 15 View

Validation of NGS taxa abundance data? or any other method (experimental or bioinoformatic based) to validate NGS results?

Hello, I have been looking out for studies which have actually tried to validate the results from NGS data. One technique I know is Real Time-PCR. I was actually looking out for real time PCR...

08 September 2018 3,203 4 View

Can any one explain Mantel Test in simple terms ?

I am trying to understand mantel test in terms of getting to a biological conclusion. I referred few papers but failed to understand it completely. I have understood that it is a correlation...

08 September 2018 5,326 1 View

Can anyone suggest me modification/s or method of DNA extraction from sediments of estuary?

I have been trying to extract DNA with no success. I have used following methods 1. PCI method with and without bead beating 2. kit methods qiagen, himedia 3. interchange of reagents 4. cold and...

11 December 2017 7,805 4 View

Can anyone explain what is meant by water memory and is there any role of electromagnetic waves in it?

03 April 2017 3,731 0 View

How one can predict the metabolic pathway using bioinformatic tools( if any) for a novel compound, if the structure of compound is known ?

source organism is also known. nearest match for structure with 80% similarity is found. is it possible?

11 December 2016 6,855 3 View

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

How to manually calculate p value in ANOVA? what is the equation or formula for it?

03 March 2021 4,928 5 View

Mixed ANOVA - help?

I'm currently working on a piece which asks to conduct an ANOVA - looking at the effect of sporting group (2 levels), and exercise trials (two trials with six levels). I've computed this all...

27 February 2021 9,626 4 View

How to Interpret Partial Eta Squared Numbers For a Repeated Measures Anova?

I have obtained Partial Eta Squared Numbers through Two-Way Mixed Anova Analysis. My results for different constructs are: .105, .135, .038, .068, .061 respectively. I wanted to know, whether...

24 February 2021 7,122 1 View

Can we proceed to perform Two-way Mixed-ANOVA despite normality violations?

While testing assumptions, Shapiro-Wilk Test failed. However, I proceeded with the analysis and the interaction effect was significant. During our course- lectures, it was mentioned that Anova...

24 February 2021 228 3 View

Sample size determination for non-parametric tests?

How do I run a a priori sample size determination for non-parametric tests, like the Mann-Whitney U-test and the Kruskall-Wallis or other non-parametric tests that accord with the unpaired t-test...

24 February 2021 166 6 View

Three-way robust ANOVA in R?

I am trying to conduct a three-way robust ANOVA in R using the WRS2 package as: t3way(Stem ~ Species*Temperature*Salinity, data = tutto) and there is an error saying : Error in if...

22 February 2021 1,674 8 View

Which test should I use in SPSS if I have two independent variables and one dependent variable that is measured using two tests?

I am researching the effect of gender and video game use on reaction times. To do this, I will have participants complete two reaction time tests (a simple test and a four choice test). I am a...

17 February 2021 9,343 4 View

Can I perform two way ANOVA in case of some missing groups?

I had control cells and performer ELISA analyses group (time 0). I stimulated cells with substance A and B and cultivated for 1, 2 and 3 hours. On each cells I performed ELISA. I have results...

17 February 2021 8,933 4 View

Level 1 pre-post multilevel regression: Panel data or ANOVA approach?

Dear colleagues, I am currently teaching myself in multilevel analysis using educational data. I found few to zero literature on basic analysis methods. In my context we frequently use level-1...

17 February 2021 9,378 5 View