MaAsLin3 total abundance scaling with basic 16S qPCR

Downstream analysis and statistics MaAsLin
1

Hello,
Really liking MaAsLin3 so far, but I had a question regarding total abundance scaling. In the paper, it looks like only spike-ins, digital PCR, or flow cytometry were used for absolute quantification. Do you still recommend using the total abundance scaling option with regular old qPCR data which isn’t as accurate as those methods?

For my dataset, we normalize all of our samples to 10 ng/ul (before library prep and qPCR), and run 16S qPCR to get 16S copies per ng of fecal DNA. Would you recommend using this value for total abundance scaling or do you think it is not precise enough?

I did run MaAsLin3 with and without using this to scale (passing the 16S copies/ng fecal DNA to unscaled_abundance with median_comparison_abundance set to FALSE for this) and got generally similar results, though is some cases certain ASVs gain/lose significance.

2

Hi @afvrbanac,

Thanks for taking a look at MaAsLin3.

qPCR data should be usable with MaAsLin3 although, results between the two methods should be fairly similar unless large variations in qPCR copy number were detected between the covariates of interest (potentially some taxa that were on the margins of significance may shift one way or another).

Cheers,
Jacob Nearing