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cafferychen777 / MicrobiomeStat

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
https://www.microbiomestat.wiki/
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Create Graphs/Analyses without Performing Rarefaction #57

Open pkirti33 opened 1 month ago

pkirti33 commented 1 month ago

Hello, I acknowledge that I have submitted several posts to this GitHub Discussions in the past few weeks, and I always appreciate your prompt and helpful replies! This package and your replies have been incredibly helpful for my analysis.

Feedback I am analyzing presence/absence microbiome data, so rarefaction is not appropriate for my project. However, I noticed that rarefaction automatically occurs when I run any analyses or create graphs. Is there a way to turn off the automatic rarefaction? If not, adding that option would be incredibly useful.

cafferychen777 commented 2 weeks ago

Hello @pkirti33,

Thank you for your continued engagement with MicrobiomeStat and for bringing this important point to our attention. We greatly appreciate your feedback as it helps us improve the package for all users.

I'm pleased to inform you that we have implemented changes based on your suggestion. We have modified the package so that automatic rarefaction no longer occurs by default for most functions. Here are the key points of the update:

  1. Automatic Rarefaction Removed: We have removed automatic rarefaction from all analysis and graphing functions, with the exception of the report functions.

  2. Report Functions: The report functions will still perform rarefaction by default. This is to ensure consistency across different analyses within a single report.

  3. Flexibility: This change provides more flexibility for users working with various types of microbiome data, including presence/absence data like yours.

We believe this update will better serve your needs and those of other researchers working with non-count data. You should be able to run your analyses and create graphs without any automatic rarefaction interfering with your presence/absence data.

If you encounter any issues or have any questions about using the updated functions, please don't hesitate to reach out. We're here to help ensure your analysis goes smoothly.

Thank you again for your valuable feedback. It's through user input like yours that we can continue to improve MicrobiomeStat and make it more versatile for different types of microbiome studies.

Best regards, Chen YANG