Error : invalid class “phyloseq” object: Component taxa/OTU names do not match.

[Saesha5]

Load necessary libraries

library(phyloseq)

metadata <- "C:/Users/Saesha Verma/OneDrive/Desktop/Analysis/Metadata_table" asv <- "C:/Users/Saesha Verma/OneDrive/Desktop/Analysis/ASV_table" taxa <- "C:/Users/Saesha Verma/OneDrive/Desktop/Analysis/Taxa_table"

Create empty lists to store data

metadata_list <- list() asv_list <- list() taxa_list <- list()

Loop through files in each directory

for (i in 1:56) {

Construct file paths

metadata_file <- paste0(metadata, "/Study", i, ".csv") asvfile <- paste0(asv, "/ASVtable.SILVA.16S", i, ".csv") taxa_file <- paste0(taxa, "/Taxadata", i, ".csv")

Read files

metadata_list[[i]] <- read.csv(metadata_file, header = TRUE, sep = ",") asv_list[[i]] <- read.csv(asv_file, header = TRUE, sep = ",") taxa_list[[i]] <- read.csv(taxa_file, header = TRUE, sep = ",")

Convert ASV data to numeric, excluding the first column if it's a row name or identifier

asv_list[[i]][, -1] <- lapply(asv_list[[i]][, -1], as.numeric) }

Convert specific columns to numeric in metadata (if necessary)

for (i in 1:56) { if (!is.numeric(metadata_list[[i]][, 1])) { metadata_list[[i]][, 1] <- as.numeric(as.character(metadata_list[[i]][, 1])) } }

Create empty list to store phyloseq objects

physeq_list <- list()

Loop through data frames and create phyloseq objects

for (i in 1:56) {

Ensure the OTU table is a numeric matrix

asv_matrix <- as.matrix(asv_list[[i]][, -1]) rownames(asv_matrix) <- asv_list[[i]][, 1] # Assuming the first column is the row names/identifiers head(taxa_names(asv_matrix))

Ensure the taxonomy table is a matrix and the row names match the OTU table

taxa_matrix <- as.matrix(taxa_list[[i]]) rownames(taxa_matrix) <- taxa_list[[i]][, 1] # Assuming the first column is the row names/identifiers

Create phyloseq object

phyloseq_1 <- phyloseq( otu_table(asv_matrix, taxa_are_rows = TRUE), sample_data(metadata_list[[i]]), tax_table(as.matrix(taxa_list[[i]])) )

Assign the phyloseq object to the list

phyloseq_list[[i]] <- phyloseq_1 }

Name each phyloseq object in the list

names(physeqlist) <- paste0("physeq", 1:56)

On running Loop through data frames to create phyloseq objects, I encounter following error Error in validObject(.Object) : invalid class “phyloseq” object: Component taxa/OTU names do not match. Taxa indices are critical to analysis. Try taxa_names()

Need to create a merged phyloseq object for 56 studies