Can qiime be used to normalize data?

[Shannon Wallace]

Hello! I am working with the diversity plots from the qiime2 16S Illumina workflow (https://github.com/LangilleLab/microbiome_helper/wiki/Amplicon-SOP-v2-(qiime2-2022.11)) and am running PERMANOVA tests on my unweighted unifrac beta diversity plots. We would like to transform out data using a centered log ratio before we performed statistical analysis on it. I was wondering if there was a way to do this using the qiime2 pathway!

Thanks,

Shannon Wallace

[Andre Comeau]

I'm not sure if there is a native way to do the transforms inside of QIIME2, however you can basically "cheat the system" to make alteration as you wish to the matrix and then rerun the QIIME2 modules:

1) Find the artifact file (*.qza) of the matrix you were using in the beta-group-significance test (such as unweighted_unifrac_distance_matrix.qza; but I suggest you drop the unweighted in favor of weighted UniFrac sicne the unweighted is known to cause potential spurious artefacts: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161196).

2) You can then access the contents of this archive (and all Q2 QZAs) by simply right-clicking (in Windows) and extracting the contents.

3) Inside you will find the matrix file in the data folder (such as distance-matrix.tsv) which you can then modify as you wish in an external program.

4) Recompress the folder/archive and then you can manipulate as you wish inside of QIIME2 again.

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Subject: [microbiome-helper] Can qiime be used to normalize data?

 

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Hello! I am working with the diversity plots from the qiime2 16S Illumina workflow (https://github.com/LangilleLab/microbiome_helper/wiki/Amplicon-SOP-v2-(qiime2-2022.11)) and am running PERMANOVA tests on my unweighted unifrac beta diversity plots. We would like to transform out data using a centered log ratio before we performed statistical analysis on it. I was wondering if there was a way to do this using the qiime2 pathway!

Thanks,

Shannon Wallace

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[Shannon Wallace]

Hi! Thanks for your help, I was able to extract the distance-matrix.tsv file and transform it using R. However, there are problems when using this file for downstream analysis. I tried to recompress the transformed file and make beta diversity plots using this workflow: https://github.com/biocore/gemelli/blob/master/ipynb/tutorials/IBD-Tutorial-QIIME2-CLI.md, but qiime gives us the error that it is not an "LSMatFormat file". Based on some further tests, we concluded that we were probably getting the error because the transformed centered log ratio distance matrix contained negative numbers. 

If anyone knows how to get around this issue somehow that would be greatly appreciated!

Thanks,

Shannon