Comments (3)
cafferychen777
commented on September 17, 2024
Dear Camuy,
I apologize for the issue you encountered while running the code. According
to the error message you provided, the problem seems to be with the
determination of the matching columns, which are used to identify the
sample name column in the metadata. I suggest checking if the column names
in `kegg_abundance` match the column that holds the sample names in the
metadata by using `colnames(kegg_abundance)`.
To resolve this issue, please follow these steps:
1. First, ensure that `metadata` contain the correct sample name column.
You can use `colnames(kegg_abundance)` and `metadata` to check their column
names.
2. Make sure that the column names in `kegg_abundance` exactly match the
column in the metadata that holds the sample names. Check for any spelling
errors or extra spaces.
3. If the column names match correctly, also ensure that the sample name
column in `metadata` does not contain any missing values. Missing values
can cause issues when subsetting columns.
If you continue to experience problems, please provide more information
about `kegg_abundance` and `metadata` so that I can assist you further.
Thank you!
…On Thu, 15 Jun 2023 at 05:45, Lennel Camuy ***@***.***> wrote:
I am running the following:
`kegg_abundance <-
ko2kegg_abundance("Dropbox/CSIRO_Picrustrun/picrust2_out_pipeline_CSIRO2/KO_predicted.tsv")
Rows: 7130 Columns: 10544
── Column specification
───────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (1): sequence
dbl (10543): K00001, K00002, K00003, K00004, K00005, K00006, K00007,
K00008, K00009, K00010, K00011, K00012...
ℹ Use spec() to retrieve the full column specification for this data.
ℹ Specify the column types or set show_col_types = FALSE to quiet this
message.
Calculation may take a long time, please be patient.
The kegg pathway with zero abundance in all the different samples has been
removed.
Perform pathway differential abundance analysis (DAA) using ALDEx2 method Please
change group to "your_group_column" if you are not using example dataset
daa_results_df2 <- pathway_daa(abundance = kegg_abundance,
-
metadata = metdata.tab,
-
group = "Treatment",
-
daa_method = "ALDEx2",
-
select = NULL,
-
reference = NULL)
Error in metadata[, matching_columns]:
! Can't subset columns with matching_columns.
✖ Subscript matching_columns can't contain missing values.
✖ It has a missing value at location 1.`
I have run metacyc analysis no problem but wanted to see why this could be?
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lcamVz
commented on September 17, 2024
Perfect! I check that out.
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cafferychen777
commented on September 17, 2024
Hello @lcamVz ,
Thank you for your input. It's indeed possible that the issue stems from the lack of one-to-one correspondence and alignment between the colnames(kegg_abundance) and the sample names in the metadata. Please double-check this aspect to ensure proper matching.
I apologize for any confusion caused, but you're right that this issue is not directly related to the ggpicrust2 package itself. It's more likely a data mismatch or alignment problem between your abundance data and metadata.
Please review the column names in the kegg_abundance object and compare them with the sample names in the metadata. Ensure that they align correctly and correspond to each other accurately. It's crucial that the sample names in the metadata match the column names in the kegg_abundance object precisely.
If you find any discrepancies or misalignments, please make the necessary adjustments to ensure the proper alignment between the two. This should help resolve the error you encountered.
If you have any further questions or need additional assistance, please let me know.
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