phyloseq
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joey711
Transform to phyloseq objects (Error in validObject(.Object) : invalid class “phyloseq” object: Component sample names do not match. Try sample_names())
Dear all,
I am new in working with Phyloseq. When I was exploring and trying to apply the phyloseq tutorial exapmle created by Daniel Vaulot (https://github.com/vaulot/R_tutorials/archive/master.zip) I faced an issue in the step of phyloseq objects transformation. This is the message I get every time I try to achieve it :
Transform to phyloseq objects
OTU = otu_table(otu_mat, taxa_are_rows = TRUE)
TAX = tax_table(tax_mat)
samples = sample_data(samples_df)
carbom <- phyloseq(OTU, TAX, samples)
carbom
Error in validObject(.Object) : invalid class “phyloseq” object: Component sample names do not match. Try sample_names() *
From what I understand, there is no match between sample_names and row.names or Rstudio failed to create the objects: OTU, TAX and samples.
Could you please help me out with this! I am struggling for 6 days in order to find the solution.
Thank you.
Aladin
P.S. I am using the tutorial's data without any changes.
I have exactly the same problem as Aladin, also with my other DADA2 results...is there something wrong with the package?
Was there a solution to this? I'm running into the same problem as well when running the tutorial.
For my data I solved the problem by changing the format of the import file to .csv and defining ";" as separator. Before I imported the meta data as text file. But I haven't tried this for the Vaulot-Tutorial.
For my data I solved the problem by changing the format of the import file to .csv and defining ";" as separator. Before I imported the meta data as text file. But I haven't tried this for the Vaulot-Tutorial.
Thanks Misemi9, this solved the problem!
I think the row.names needs to be assigned after using sample_data I followed the link below to solve the problem. https://github.com/joey711/phyloseq/issues/1020
Dear friends
I am sorry for bringing this topic again. I am new to Rstudio I have the same issue and can't solve it I have tried everything you have mentioned, but still the same mistake
I run
otu <- read.table(file = "feature-table.tsv", sep = "\t", header = T, row.names = 2, skip = 1, comment.char = "") taxonomy <- read.table(file = "taxonomy.tsv", sep = "\t", header = T ,row.names = 1)
clean the taxonomy, Greengenes format
tax <- taxonomy %>% select(Taxon) %>% separate(Taxon, c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"), "; ")
tax.clean <- data.frame(row.names = row.names(tax), Kingdom = str_replace(tax[,1], "k__",""), Phylum = str_replace(tax[,2], "p__",""), Class = str_replace(tax[,3], "c__",""), Order = str_replace(tax[,4], "o__",""), Family = str_replace(tax[,5], "f__",""), Genus = str_replace(tax[,6], "g__",""), Species = str_replace(tax[,7], "s__",""), stringsAsFactors = FALSE)
tax.clean[is.na(tax.clean)] <- "" tax.clean[tax.clean=="__"] <- ""
for (i in 1:nrow(tax.clean)){ if (tax.clean[i,7] != ""){ tax.clean$Species[i] <- paste(tax.clean$Genus[i], tax.clean$Species[i], sep = " ") } else if (tax.clean[i,2] == ""){ kingdom <- paste("Unclassified", tax.clean[i,1], sep = " ") tax.clean[i, 2:7] <- kingdom } else if (tax.clean[i,3] == ""){ phylum <- paste("Unclassified", tax.clean[i,2], sep = " ") tax.clean[i, 3:7] <- phylum } else if (tax.clean[i,4] == ""){ class <- paste("Unclassified", tax.clean[i,3], sep = " ") tax.clean[i, 4:7] <- class } else if (tax.clean[i,5] == ""){ order <- paste("Unclassified", tax.clean[i,4], sep = " ") tax.clean[i, 5:7] <- order } else if (tax.clean[i,6] == ""){ family <- paste("Unclassified", tax.clean[i,5], sep = " ") tax.clean[i, 6:7] <- family } else if (tax.clean[i,7] == ""){ tax.clean$Species[i] <- paste("Unclassified ",tax.clean$Genus[i], sep = " ") } }
metadata <- read.table(file = "sample-metadata.tsv", sep = "\t", header = T, row.names = 1) OTU = otu_table(as.matrix(otu), taxa_are_rows = TRUE) TAX = tax_table(as.matrix(tax.clean)) SAMPLE <- sample_data(metadata) TREE = read_tree("tree.nwk")
merge the data
ps <- phyloseq(OTU, TAX, SAMPLE,TREE)
and got
Error in validObject(.Object) : invalid class “phyloseq” object: Component sample names do not match. Try sample_names()
Maybe because the first name of the sample(1rA) is cut by the program And I can't figure out how to keep it (pic-Rstudio)
There are some screenshots Samples name not in order, they mixed up, I have 72 samples
I would appreciate any help
@ShevchenkoAlla The error you are getting is probably that the sample names in the otu table and metadata files are not matching.
@ShevchenkoAlla The error you are getting is probably that the sample names in the otu table and metadata files are not matching.
Thank you) But as I mentioned before the sample names are not in order in otu table, I don't know why qiime2 made them that way, they just mixed up.
Everything should be matched
t way)
Hi, I had the same issue.
Error in validObject(.Object) : invalid class “phyloseq” object: Component sample names do not match. Try sample_names()
For me, the issue was solved by specifying what column my row names are in, so phyloseq knows what to match the otu_table to. It was mentioned in one of the comments above. When you are importing your metadata (CSV-file), you need to specify seperators and row.names (in my case, first column, so row.names = 1).
This is the whole code I used to create a phyloseq object (that worked for me):
#Based on http://benjjneb.github.io/dada2/tutorial.html "Handsoff phyloseq"
Aim: Create a phyloseq object with all data for further analysis
Load required packages
library(phyloseq) library(Biostrings) library(ggplot2) library(readxl) theme_set(theme_bw())
Load taxonomic assignment and otu table (rds files need to be imported to R and stored as an object)
taxa <- readRDS("/Users/admin/HPC/12-07-23/taxonomy_table.rds") seqtab.nochim <- readRDS("/Users/admin/HPC/12-07-23/sequence_table.rds")
Load the metadata (CSV file) into a data frame
metadata <- read.csv("/Users/admin/metadata/metadata_microbiome_27.09.23.csv", sep = ";", row.names = 1)
Create the phyloseq object
ps <- phyloseq( otu_table(seqtab.nochim, taxa_are_rows = FALSE), sample_data(metadata), # Use the 'sample_names' column from the metadata data frame tax_table(taxa) # Include taxonomic information if available )
...
Hi all,
I am currently facing an issue while working with the microbiome package in R and would greatly appreciate your insights.
# I will copy code from terminal here
> b.lgg <- divergence(subset_samples(physeq, Description == "Stool_controls"),
+ apply(abundances(subset_samples(physeq, Description == "Stool_controls")), 1, median))
> b.pla <- divergence(subset_samples(physeq, Description == "Stool_samples"),
+ apply(abundances(subset_samples(physeq, Description == "Stool_samples")), 1, median))
Error in validObject(.Object) : invalid class “phyloseq” object:
Component sample names do not match.
Try sample_names()
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Athens
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] jeevanuDB_0.0.01 RColorBrewer_1.1-3 lubridate_1.9.3
[4] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[7] purrr_1.0.2 readr_2.1.4 tidyr_1.3.0
[10] tibble_3.2.1 tidyverse_2.0.0 knitr_1.45
[13] microbiome_1.24.0 ggplot2_3.4.4 devtools_2.4.5
[16] usethis_2.2.2 BiocManager_1.30.22 phyloseq_1.46.0
loaded via a namespace (and not attached):
[1] bitops_1.0-7 remotes_2.4.2.1
[3] permute_0.9-7 rlang_1.1.2
[5] magrittr_2.0.3 ade4_1.7-22
[7] compiler_4.3.1 mgcv_1.9-0
[9] vctrs_0.6.5 reshape2_1.4.4
[11] profvis_0.3.8 pkgconfig_2.0.3
[13] crayon_1.5.2 fastmap_1.1.1
[15] XVector_0.42.0 ellipsis_0.3.2
[17] caTools_1.18.2 utf8_1.2.4
[19] promises_1.2.1 tzdb_0.4.0
[21] sessioninfo_1.2.2 xfun_0.41
[23] zlibbioc_1.48.0 cachem_1.0.8
[25] GenomeInfoDb_1.38.1 jsonlite_1.8.8
[27] biomformat_1.30.0 later_1.3.2
[29] rhdf5filters_1.14.1 Rhdf5lib_1.24.1
[31] parallel_4.3.1 cluster_2.1.6
[33] R6_2.5.1 stringi_1.8.3
[35] pkgload_1.3.3 Rcpp_1.0.11
[37] iterators_1.0.14 IRanges_2.36.0
[39] timechange_0.2.0 httpuv_1.6.13
[41] Matrix_1.6-4 splines_4.3.1
[43] igraph_1.6.0 tidyselect_1.2.0
[45] rstudioapi_0.15.0 vegan_2.6-4
[47] gplots_3.1.3 codetools_0.2-19
[49] miniUI_0.1.1.1 pkgbuild_1.4.3
[51] lattice_0.22-5 plyr_1.8.9
[53] Biobase_2.62.0 shiny_1.8.0
[55] withr_2.5.2 Rtsne_0.17
[57] survival_3.5-7 urlchecker_1.0.1
[59] Biostrings_2.70.1 pillar_1.9.0
[61] KernSmooth_2.23-22 foreach_1.5.2
[63] stats4_4.3.1 generics_0.1.3
[65] RCurl_1.98-1.13 hms_1.1.3
[67] S4Vectors_0.40.2 munsell_0.5.0
[69] scales_1.3.0 gtools_3.9.5
[71] xtable_1.8-4 glue_1.6.2
[73] tools_4.3.1 data.table_1.14.10
[75] fs_1.6.3 rhdf5_2.46.1
[77] grid_4.3.1 ape_5.7-1
[79] colorspace_2.1-0 nlme_3.1-164
[81] GenomeInfoDbData_1.2.11 cli_3.6.2
[83] fansi_1.0.6 gtable_0.3.4
[85] digest_0.6.33 BiocGenerics_0.48.1
[87] htmlwidgets_1.6.4 memoise_2.0.1
[89] htmltools_0.5.7 multtest_2.58.0
[91] lifecycle_1.0.4 mime_0.12
[93] MASS_7.3-60
The code showed above attempts to calculate divergence for subsets of my phyloseq object based on sample descriptions ("Stool_controls" and "Stool_samples").
I have verified that the sample names within each subset match using:
# I will copy code from terminal here
> rownames(sample_data(physeq))
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11"
[12] "12" "13" "14" "15" "16" "17" "18" "19" "20" "21" "22"
[23] "23" "24" "25" "26" "27" "28" "29" "30" "31" "32" "33"
[34] "34" "35" "36" "37" "38" "39" "40" "41" "42" "43" "44"
[45] "45" "46" "47" "48" "49" "C1" "C2" "C4" "C5" "C6" "C7"
[56] "C8" "C9" "C10" "C11" "C12" "C13" "C14" "C15" "C16" "C17" "C18"
[67] "C19" "C20" "C21" "C22" "C23" "C24" "C25" "C26" "C27" "C28" "C29"
[78] "C30" "C31" "C32" "C33" "C34" "C35" "C36" "C37" "C38" "C39" "C40"
[89] "C41" "C42" "C43" "C44" "C45" "C46" "C47"
> sample_names(physeq)
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11"
[12] "12" "13" "14" "15" "16" "17" "18" "19" "20" "21" "22"
[23] "23" "24" "25" "26" "27" "28" "29" "30" "31" "32" "33"
[34] "34" "35" "36" "37" "38" "39" "40" "41" "42" "43" "44"
[45] "45" "46" "47" "48" "49" "C1" "C2" "C4" "C5" "C6" "C7"
[56] "C8" "C9" "C10" "C11" "C12" "C13" "C14" "C15" "C16" "C17" "C18"
[67] "C19" "C20" "C21" "C22" "C23" "C24" "C25" "C26" "C27" "C28" "C29"
[78] "C30" "C31" "C32" "C33" "C34" "C35" "C36" "C37" "C38" "C39" "C40"
[89] "C41" "C42" "C43" "C44" "C45" "C46" "C47"
If anyone has encountered a similar issue or has insights into why this might be happening, I would greatly appreciate your help.
If there are alternative approaches to calculate divergence for specific sample subsets in phyloseq, I am open to suggestions.
Thank you in advance for your time and assistance.
