number of samples for differential abundance analysis

General Discussion
1

Dear all,

when i was working on my soil 16 amplicon sequencing data (12 samples taken for 2 treatements), by looking at the Pcoa plot of weighted UniFrac distances, i discovered one sample isolated from all the others and noticed this sample has very high levels of phosphorus compared to the others.
I then tried DA analysis (ALDEx2 in R studio ggpicrust2) on the q2 picrust2 functional annotated data to confirm my hypothesis but i think i cannot perform it becouse it is just one sample and i think i need at least 3 per group. Can anyone suggest me a way to discover differentally abundant OTUs or functional annotations for 1 sample vs all? or other ways to analyze the same data?

thanks in advance,

Michele

i will report my error here just in case:

computing center with all features
Error in apply(data[, grp2], 1, sd) : dim(X) must have a positive length

2

Hi @Michele94,

You could potentially analyze the phospherous concentration as continuous (ANCOM-BC will let you use a continuous predictor) and then you won't have 1 group vs many, you'll have everything in a continous distribution.

However, I still think you're going to have issues with 12 samples along a continous distribution. You may be limited in your interence and may need to focus on descriptive analyses.

Best,
Justine

3 Likes
3

Ok, i'll try both then. thank you for the suggestion!