Replies: 2 comments 1 reply
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Dear Niall, Thank you for your questions regarding the rarefaction process in MicrobiomeStat. I'm happy to provide some clarification.
Your observation is valuable, and if there's an issue with the function, we'd like to address it promptly. Thank you for bringing this to our attention. Your feedback helps us improve MicrobiomeStat. Best regards, |
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Hi Chen, Thanks for your reply. Looking at the rarefied data again, it's actually 5 out of 36 columns that had their values changed to zeroes, but I can't Here I've attached the my feature.tab abundance file, my feature.ann file, and my metadata, before and after I rarefied them. Let me know if the attachments didn't work. Thanks! SEM.bact.abun.copies.per.gram.feature.tab.csv SEM.bact.abun.copies.per.gram.feature.tab.rarefied.csv |
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Hi Chen,
I was just wondering why it's recommended to rarefy data before calculating measures of diversity?
I used mStat_rarefy_data, and it seems to have dropped some species from my abundance data. Is that normal? I also noticed that some of the columns in my abundance table have had their values all changed to zero. Is that a mistake?
Thanks!
-Niall
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