can i used --p-pairwise and --p-no-pairwise in the same command and what is the best for my data as my data is different sources of bacteria (note: not all sources related to other)

Hi @hasnaa,

the two options are mutually exclusive, you can use ‘–p-pairwise’ if you like to perform pairwise tests between all pairs of groups. If I recall correctly, the ‘–pairwise’ option performs the comparisons between samples in a group and itself, adding these to the visualiser. Hence, if you have lots of group, it takes longer and the final box plot picture may be too ‘crowded’.

But you can try with and without the ‘–pairwise’ option to see the difference!

If you don’t specify ‘–p-pairwise’ the, ‘–p-no-pairwise’ is the default.

Hope it helps

Hi, IIenzi thanks for your support but I tried two options and no difference between them is that true and no problem or what🤔

Hi @hasnaa,

I expect that the two results be the same in terms of statistics and p-values, I would expect more box-plots in the visualisers by using the ‘–p-pairwise’ option.

Would you share both the commands and the resulting ‘qzv’ files?

(you can message me privately the qzv if you don’t like for them to be public)

Cheers