KO metagenome output in %

[Dr. Lekha Menon Margassery]

Dear Gavin,

I have a doubt in PICRUSt 2.0. I have the KO_metagenome_out file. I have attached a subset of that file. I have seen in research papers that the raw data (relative abundance) is converted to percentage. Can you please help me figure out how to do this? 

The analysis is done in QIIME 2 and greengenes dataset 'gg_13_8_otus'. 

Your help is much appreciated. 

Regards,

Lekha

[Gavin Douglas]

Hi there,

To convert the data to percentages you would you would divide each column by the total abundance for that column and then multiply it by 100. Does that make sense? In other words, the data is normalized per sample.

Cheers,

Gavin

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[Dr. Lekha Menon Margassery]

Hi Gavin,

Thanks for your prompt reply. So, you mean to say, I will have to add all the abundances across the samples (which means rows) and then multiply by 100 as all pathway is different in the samples, isn't? So, from the example file (in which I have done the calculation for one of them), it would be something similar to what I have highlighted in yellow, isn't? 

Your help is much appreciated. 

Regards,

Lekha

[Gavin Douglas]

Hey Lekha,

No the normalization is usually done by sample - so that you can compare the % of each pathway found within a sample (i.e. you would sum all pathway abundances for a sample). This is what is meant by relative abundance when discussing microbiome features (whether pathways, OTUs, species, etc)

Cheers,

Gavin

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[Dr. Lekha Menon Margassery]

Hi Gavin,

That makes more sense. Thanks a lot. So, its column and not rows then. Thanks once again. 

Regards,

Lekha