cafferychen777
commented
1 year ago Hello,
It seems that there might be an issue with the data structure of your metadata. The metadata should be a tibble, and I noticed that you mentioned the sample name should be a column in the tibble.
To resolve the error you encountered, which states that the subscript matching_columns can't contain missing values, with a missing value at location 1, please make sure that your metadata is properly structured. Here are a few steps you can follow:
-
Confirm that your metadata is in tibble format. If it's not, you can convert it to a tibble using the
as_tibble()function. For example:metadata <- as_tibble(metadata). -
Check the structure of your metadata tibble and ensure that the sample name column exists. You can use the
str()function to examine the structure of your metadata, like this:str(metadata). Make sure that the first column contains the sample names and that the following columns represent the corresponding groups. -
Verify that the sample names in your metadata tibble match the column names in the
kegg_abundanceobject. You can use thecolnames()function to compare the column names, like this:metadata[,sample_name]andcolnames(kegg_abundance).
If the column names in your metadata and kegg_abundance do not match, you need to ensure that the sample names are correctly aligned. However, please note that transposing the metadata and making the sample name a column might not be the appropriate solution, as it may result in the loss of sample grouping information.
Additionally, I noticed that you are using an older version of ggpicrust2. To ensure you have the latest bug fixes and improvements, I recommend upgrading to the newest version available on GitHub using the following command: devtools::install_github('cafferychen777/ggpicrust2').
If you have followed these steps and are still encountering the issue, it would be helpful for further debugging if you could provide the dataset you are working with. By examining the actual data, I can better understand the structure and identify any potential issues that may be causing the error. Please provide the path_abun_unstrat.tsv and Metadata.txt files or any relevant sample data that can help in reproducing the problem.
Once I have access to the dataset, I will be able to assist you more effectively in resolving the issue. Please attach the files or provide a link to the dataset if possible.
Please let me know if you need any further assistance!
mayagabitzsch
hello, I am trying to follow the example code with my data. I used the file path_abun_unstrat.tsv and a file titled Metadata.txt When I try to run the ggpicrust with the input file path, I get an error stating that the subscript matching columns can't contain missing values, It has a missing value at location 1. Here is what the code Looks like
and the error that is given is
Calculation may take a long time, please be patient. The kegg pathway with zero abundance in all the different samples has been removed. Performing pathway differential abundance analysis... Error inmetadata[, matching_columns]: ! Can't subset columns withmatching_columns. ✖ Subscriptmatching_columnscan't contain missing values. ✖ It has a missing value at location 1. Runrlang::last_trace()` to see where the error occurred.I went through the step by step approach in the read me and this is the command where the error is popping up
daa_results_df <- pathway_daa(abundance = kegg_abundance, metadata = metadata, group = "ENVIRONMENT", daa_method = "ALDEx2", select = NULL, reference = NULL)I found another post that had the same error as me, and I tried to follow the advice there and the issue is still not resolving. I am not sure if I am understanding the solutions correctly. I transposed my metadata file so that the sample name was the columns, matching the kegg_abundance, The first column in my meta data is the sample_name with the following groups I am putting my data in. That column does not show up on the kegg abundance columns and I think that might be the issue? But then I lose my samples groupings. I am unsure how to make them match.