All my pathway results are NA

[weiGu-88]

Hi,
First of all, thanks for creating this tool.I encountered the same issue as #106.Could you please provide a code modification strategy? Thank you for your response.

[weiGu-88]

Could you please explain the reason behind the error 'Error in aldex.clr.function(reads, conds, mc.samples, denom, verbose, : rownames(reads) cannot be empty' and suggest how to modify the code to resolve it?

[cafferychen777]

Hi @weiGu-88,

Thank you for reporting this issue. The error Error in aldex.clr.function(reads, conds, mc.samples, denom, verbose): rownames(reads) cannot be empty typically occurs due to a few common reasons:

1. Data Format Issues

# Check your data structure first
print(head(kegg_abundance))
print(dim(kegg_abundance))
print(head(rownames(kegg_abundance)))

# Ensure proper row names
if (is.null(rownames(kegg_abundance))) {
  # If your first column contains pathway IDs
  kegg_abundance <- kegg_abundance %>%
    column_to_rownames("pathway") # or whatever your pathway ID column is named
}

2. Data Transformation Fix

# Make sure your abundance data is properly formatted
kegg_abundance <- as.data.frame(kegg_abundance)

# Remove any rows with all zeros
kegg_abundance <- kegg_abundance[rowSums(kegg_abundance) > 0, ]

# Ensure numeric values
kegg_abundance <- mutate_all(kegg_abundance, as.numeric)

3. Complete Working Example

library(tidyverse)
library(ggpicrust2)

# Load and prepare data
kegg_abundance <- ko2kegg_abundance("your_file.tsv")

# Verify data structure
stopifnot(!is.null(rownames(kegg_abundance)))
stopifnot(nrow(kegg_abundance) > 0)

# Perform pathway analysis
daa_results_df <- pathway_daa(
    abundance = kegg_abundance,
    metadata = metadata,
    group = "group",
    daa_method = "ALDEx2",
    select = NULL,
    reference = NULL
)

Additional Troubleshooting Tips:

1. Make sure your abundance data contains no negative values
2. Verify that your metadata group column matches exactly with your sample names
3. Consider using print(str(kegg_abundance)) to inspect the data structure

If you could share a small sample of your data (first few rows/columns), I can provide more specific guidance.

Best regards,
Chen Yang