Question about ASV abundance

Hi everyone I am trying to prepare my data for network analysis using MENA ( I am using the aggregate function in R to collapse the ASVs into their assigned taxonomy and I get 52 ASVs. Phyloseq is telling me I have over 100 in some of my treatments when I do my alpha diversity analysis. This is for archaea by the way

I'm not sure why this is?

I hope my question makes sense.

Best wishes

The default na.action of aggregate is to ignore missing values in the given variables.

Thank you for the reply yilewu,

But wouldn't that mean that i should keep the 100 species that phyloseq is telling me i have? or am i misunderstanding.

Are you aware of a way in which i can keep these species or am i just doing this wrong?

Best wishes

It means aggregate will remove the rows(ASV) that contain 'NA'. I think dplyr::summarise would be a better choice.

ASVs %>%
group_by(taxonomy) %>%
summarise_all(sum) -> data

Thank you for helping me with this :slight_smile:

I got the same problem though. I am not sure what is going on. I know i have over 100 observed species according to qiime2 , phyloseq and ampvis2 so i have no idea why i am losing them when trying to aggregate them together.

Best wishes

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