phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
I'm running into issues when trying to create my phyloseq object. Using the code below normally works for me and I haven't changed anything, but I keep running into the same error when loading my metadata file in.
Error in read.table("/work/jennifer.bowen/Brian/Pulse Press 2022/Run 1/Tufts_Run1_metadata.txt", :
duplicate 'row.names' are not allowed
The first column in the metadata is SampleID and I've checked many times that each sampleID is 100% unique from any others without special characters (ex sample ID: 1AF0DNA). I'm not quite sure. I've attached a screenshot of a portion of the metadata text file. any suggestions?
Hi there,
I'm running into issues when trying to create my phyloseq object. Using the code below normally works for me and I haven't changed anything, but I keep running into the same error when loading my metadata file in.
mat1 = read.table("/work/jennifer.bowen/Brian/Pulse Press 2022/Run 1/ASVs_counts.tsv", header = TRUE, sep = "\t", row.names = 1) tax1 = read.table("/work/jennifer.bowen/Brian/Pulse Press 2022/Run 1/ASVs_taxonomy.tsv", header = TRUE, sep = "\t", row.names = 1) meta1 = read.table("/work/jennifer.bowen/Brian/Pulse Press 2022/Run 1/Tufts_Run1_metadata.txt", header = TRUE, sep = "\t", row.names = 1)
Error in read.table("/work/jennifer.bowen/Brian/Pulse Press 2022/Run 1/Tufts_Run1_metadata.txt", : duplicate 'row.names' are not allowed
The first column in the metadata is SampleID and I've checked many times that each sampleID is 100% unique from any others without special characters (ex sample ID: 1AF0DNA). I'm not quite sure. I've attached a screenshot of a portion of the metadata text file. any suggestions?