Anbu Poosakkannu

Thanks, I could do that. Just want to get extra than that to get prevalence based on a factor. I mean to get abundance and prevalence for each sample and/or...

I am not much familiar with for cycle. I tried and it did not work. Could you please give me some toy example? Thanks in advance!

Hi, Something like below example in phyloseq object, GP.chl = subset_taxa(GlobalPatterns, Phylum=="Chlamydiae")

Thanks. It kind of worked, but i have problem when i do the differential abundance analysis. I have the following codes for my analysis in which when i subset the...

Thanks, but it will be not original abundance right? because i subset only specific taxa! Please let me know if i can just plot taxa g__Campylobacter without any subset?

Thanks. it worked.

Hi, I wonder could it be possible to subset some taxa without affecting their original abundance or count for the alpha and beta diversity analysis.

I need to get the microeo obiect data only for following potential pathogenic genus, g__Acinetobacter|g__Aeromonas|g__Anaplasma|g__Bacillus|g__Bartonella|g__Borrelia|g__Campylobacter|g__Chlamydia|g__Citrobacter|g__Clostridiodes|g__Clostridium|g__Corynebacterium|g__Coxiella|g__Ehrilchia|g__Enterobacter|g__Enterococcus|g__Escherichia|g__Francisella|g__Klebsiella|g__Listeria|g__Mycobacterium|g__Mycoplasma|g__Neoehrilchia|g__Pasteurella|g__Proteus|g__Pseudomonas|g__Rickettsia|g__Salmonella|g__Serratia|g__Staphylococcus|g__Streptococcus|g__Vibrio|g__Yersinia' and then proceed with normal analysis such as alpha and beta diversity. On Wed, Nov...

actually something like here in the link, https://github.com/joey711/phyloseq/issues/1048 On Wed, Nov 16, 2022 at 9:05 AM Anbu Poosakkannu ***@***.***> wrote: > I need to get the microeo obiect data only...

Thanks. The subseeting of taxa worked. But it did not affect the alpha and beta diversity calculations. They remain the same as original data. On Wed, Nov 16, 2022 at...