0 features are filtered! #119
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Hi all, I'm having my first go trying to run ggpicrust2 with some bacterial abundance data from an orchard. I'm inputting the abundance data with the species names to identify the rows. My metadata file is identifying the treatment group for each sample. I'm trying to replicate the example from the CRAN README page. Here's the code I'm using: And here's the console readout I get when I run this code: Anyone know what's going wrong here? Thanks! |
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Replies: 4 comments 2 replies
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Dear @niall142, Thank you for reaching out about the issue you're experiencing with ggpicrust2. I appreciate you providing the code and console output, but without access to your actual data files, it's challenging to pinpoint the exact cause of the problem. To help me debug this issue more effectively, would you be willing to send your data files to cafferychen777@tamu.edu? Specifically, it would be helpful to have:
With these files, I'll be able to reproduce the error and investigate what might be causing the "0 features are filtered" issue and the subsequent error. Please ensure to remove any sensitive information from the files before sending them. Once I receive the data, I'll take a closer look and get back to you with more specific guidance. Thank you for your patience and cooperation in resolving this issue. Best regards, |
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Hi Chen,
Thanks very much for your reply, I've attached my abundance data and my
metadata files here. As in the readme example, I've saved the abundance
data as a .tsv file, and the metadata as .txt, but I wasn't sure whether
that's a specific requirement of ggpicrust or not. I'm also not entirely
sure I have the right format; does it matter for picrust whether you use
copies-per-gram abundance data, or another form? Are the species names of
the bacteria sufficient for the database search?
Thanks!
-Niall
On Mon, Sep 23, 2024 at 12:15 AM Caffery Yang ***@***.***> wrote:
Dear @niall142 <https://github.com/niall142>,
Thank you for reaching out about the issue you're experiencing with
ggpicrust2. I appreciate you providing the code and console output, but
without access to your actual data files, it's challenging to pinpoint the
exact cause of the problem.
To help me debug this issue more effectively, would you be willing to send
your data files to ***@***.***? Specifically, it would be
helpful to have:
1. Your bacterial abundance data file
(SEM.bacteria.cpg.2024.rename.test)
2. Your metadata file (SEM.soil.samples.IDs.2024)
With these files, I'll be able to reproduce the error and investigate what
might be causing the "0 features are filtered" issue and the subsequent
error.
Please ensure to remove any sensitive information from the files before
sending them. Once I receive the data, I'll take a closer look and get back
to you with more specific guidance.
Thank you for your patience and cooperation in resolving this issue.
Best regards,
Chen YANG
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plot.ID trial row mulch.treatment mulch.treatment.flag year code plot.ID.year
SEM.R1.con SEM R1 con white 2024 CU600O SEM.R1.con.2024
SEM.R1.new SEM R1 new yellow 2024 CU600P SEM.R1.new.2024
SEM.R1.old SEM R1 old pink 2024 CU600Q SEM.R1.old.2024
SEM.R2.old SEM R2 old pink 2024 CU600R SEM.R2.old.2024
SEM.R2.new SEM R2 new yellow 2024 CU600S SEM.R2.new.2024
SEM.R2.con SEM R2 con white 2024 CU600T SEM.R2.con.2024
SEM.R3.new SEM R3 new yellow 2024 CU600U SEM.R3.new.2024
SEM.R3.con SEM R3 con white 2024 CU600V SEM.R3.con.2024
SEM.R3.old SEM R3 old pink 2024 CU600W SEM.R3.old.2024
SEM.R4.new SEM R4 new yellow 2024 CU600X SEM.R4.new.2024
SEM.R4.old SEM R4 old pink 2024 CU600Y SEM.R4.old.2024
SEM.R4.con SEM R4 con white 2024 CU600Z SEM.R4.con.2024
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Dear Niall, Thank you for your response and for attempting to share your data files. Unfortunately, it seems there was an issue with uploading the data to GitHub. The discussion thread only shows the metadata content, but the abundance data file is missing. Given these limitations with GitHub, I suggest sending your data files directly to my email address: cafferychen777@tamu.edu. This will ensure I receive both the abundance data and the metadata files in their entirety. Please include the following in your email:
Once I receive these files, I'll be able to thoroughly examine your data and provide more specific guidance on resolving the "0 features are filtered" issue you're experiencing with ggpicrust2. Thank you for your patience and cooperation. I look forward to helping you resolve this problem. Best regards, |
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Woops, my mistake, I sent the files to your email there now.
Thanks!
-Niall
…On Mon, Sep 23, 2024 at 9:41 AM Caffery Yang ***@***.***> wrote:
Dear Niall,
Thank you for your response and for attempting to share your data files.
Unfortunately, it seems there was an issue with uploading the data to
GitHub. The discussion thread only shows the metadata content, but the
abundance data file is missing.
Given these limitations with GitHub, I suggest sending your data files
directly to my email address: ***@***.*** This will ensure I
receive both the abundance data and the metadata files in their entirety.
Please include the following in your email:
1. The bacterial abundance data file
(SEM.bacteria.cpg.2024.rename.test)
2. The metadata file (SEM.soil.samples.IDs.2024)
Once I receive these files, I'll be able to thoroughly examine your data
and provide more specific guidance on resolving the "0 features are
filtered" issue you're experiencing with ggpicrust2.
Thank you for your patience and cooperation. I look forward to helping you
resolve this problem.
Best regards,
Chen Yang
—
Reply to this email directly, view it on GitHub
<#119 (reply in thread)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ARY3AFZEVKPWZETYU5Q6ZKLZYBAC7AVCNFSM6AAAAABOSZVR52VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANZSHA4TGNQ>
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You are receiving this because you were mentioned.Message ID:
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Dear Niall, Thank you for sending your data files and for your patience as we work through this issue. After reviewing your files, I believe I've identified the source of the problem. It appears there may have been a misunderstanding about the type of data ggpicrust2 is designed to work with. The package is specifically tailored for use with data generated by PICRUSt2, which provides functional predictions based on 16S rRNA gene sequences. The bacterial abundance data you've provided, while valuable, is not the type of input ggpicrust2 is optimized to process. While it is possible to use ggpicrust2 with your data, it may not be the most efficient or appropriate tool for your specific analysis needs. Instead, I'd like to recommend an alternative that might be more suitable for your bacterial abundance data. I suggest you take a look at the MicrobiomeStat package. This package offers both differential abundance analysis and visualization tools that are well-suited to the type of data you're working with. You can find more information about MicrobiomeStat at www.microbiomestat.wiki. In particular, I think you might find the section on cross-sectional taxa analysis especially relevant to your needs. You can find this information here: This resource should provide you with guidance on how to perform the kind of analysis you're looking for, using tools that are more appropriate for your bacterial abundance data. If you have any questions about using MicrobiomeStat or need further clarification, please don't hesitate to ask. I'm here to help you find the best solution for your research needs. Best regards, |
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Hi Chen,
Thanks very much for taking a look for me, that's a big help! I'll take a
look at MicrobiomeStat, thanks for the recommendation.
…-Niall
On Tue, Sep 24, 2024 at 7:59 AM Caffery Yang ***@***.***> wrote:
Dear Niall,
Thank you for sending your data files and for your patience as we work
through this issue. After reviewing your files, I believe I've identified
the source of the problem.
It appears there may have been a misunderstanding about the type of data
ggpicrust2 is designed to work with. The package is specifically tailored
for use with data generated by PICRUSt2, which provides functional
predictions based on 16S rRNA gene sequences. The bacterial abundance data
you've provided, while valuable, is not the type of input ggpicrust2 is
optimized to process.
While it is possible to use ggpicrust2 with your data, it may not be the
most efficient or appropriate tool for your specific analysis needs.
Instead, I'd like to recommend an alternative that might be more suitable
for your bacterial abundance data.
I suggest you take a look at the MicrobiomeStat package. This package
offers both differential abundance analysis and visualization tools that
are well-suited to the type of data you're working with. You can find more
information about MicrobiomeStat at www.microbiomestat.wiki.
In particular, I think you might find the section on cross-sectional taxa
analysis especially relevant to your needs. You can find this information
here:
https://www.microbiomestat.wiki/single-point-analysis/cross-sectional-investigation-taxa-analysis-with-microbiomestat
This resource should provide you with guidance on how to perform the kind
of analysis you're looking for, using tools that are more appropriate for
your bacterial abundance data.
If you have any questions about using MicrobiomeStat or need further
clarification, please don't hesitate to ask. I'm here to help you find the
best solution for your research needs.
Best regards,
Chen Yang
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Reply to this email directly, view it on GitHub
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Dear Niall,
Thank you for sending your data files and for your patience as we work through this issue. After reviewing your files, I believe I've identified the source of the problem.
It appears there may have been a misunderstanding about the type of data ggpicrust2 is designed to work with. The package is specifically tailored for use with data generated by PICRUSt2, which provides functional predictions based on 16S rRNA gene sequences. The bacterial abundance data you've provided, while valuable, is not the type of input ggpicrust2 is optimized to process.
While it is possible to use ggpicrust2 with your data, it may not be the most efficient or appropriate tool for your specific anal…