Component sample names do not match. Try sample_names().

[abalter]

This section of the workflow is throwing an error:

library(phyloseq)
ps <- phyloseq(otu_table(seqtabNoC, taxa_are_rows=FALSE), 
               sample_data(samdf), 
               tax_table(taxTab),phy_tree(fitGTR$tree))
ps <- prune_samples(sample_names(ps) != "Mock", ps) # Remove mock sample
ps

The error is:

Error in validObject(.Object) : invalid class “phyloseq” object: Component sample names do not match. Try sample_names()

I'm pretty sure I've gotten through the sample workflow without this error. Can someone tell me exactly which row or column names are supposed to be matching but are not?

These are the rownames of my variables:

> rownames(otu_table(seqtabNoC, taxa_are_rows=FALSE))
 [1] "F3D0"   "F3D1"   "F3D141" "F3D142" "F3D143" "F3D144" "F3D145" "F3D146" "F3D147" "F3D148" "F3D149" "F3D150"
[13] "F3D2"   "F3D3"   "F3D5"   "F3D6"   "F3D7"   "F3D8"   "F3D9"  
> rownames(sample_data(samdf))
 [1] "NA"    "NA.1"  "NA.2"  "NA.3"  "NA.4"  "NA.5"  "NA.6"  "NA.7"  "NA.8"  "NA.9"  "NA.10" "NA.11" "NA.12"
[14] "NA.13" "NA.14" "NA.15" "NA.16" "NA.17" "NA.18"
> rownames(phy_tree(fitGTR$tree))
NULL

[benjjneb]

Can someone tell me exactly which row or column names are supposed to be matching but are not?

The samdf data.frame should have rownames matching those of the otu_table, e.g. "F3D0", "F3D1", ...

[abalter]

Hey @benjjneb -- Still having a problem. Somehow, the samdf object is getting, to put it technically, messed up.

> samdf <- read.csv("http://raw.githubusercontent.com/spholmes/F1000_workflow/master/data/MIMARKS_Data_combined.csv",header=TRUE)
> head(samdf)
> #summary(samdf)
> samdf$SampleID <- paste0(gsub("00", "", samdf$host_subject_id), "D", samdf$age-21)
> #summary(samdf)
> samdf <- samdf[!duplicated(samdf$SampleID),] # Remove dupicate entries for reverse reads
> head(samdf)
> #summary(samdf)
> rownames(seqtabAll) <- gsub("124", "125", rownames(seqtabAll)) # Fix discrepancy
> all(rownames(seqtabAll) %in% samdf$SampleID) # TRUE
[1] TRUE
> rownames(samdf) <- samdf$SampleIDlib
> keep.cols <- c("collection_date", "biome", "target_gene", "target_subfragment",
+ "host_common_name", "host_subject_id", "age", "sex", "body_product", "tot_mass",
+ "diet", "family_relationship", "genotype", "SampleID") 
> print(keep.cols)
 [1] "collection_date"     "biome"               "target_gene"         "target_subfragment" 
 [5] "host_common_name"    "host_subject_id"     "age"                 "sex"                
 [9] "body_product"        "tot_mass"            "diet"                "family_relationship"
[13] "genotype"            "SampleID"           
> samdf <- samdf[rownames(seqtabAll), keep.cols]
> head(samdf)
> #summary(samdf)
> rownames(samdf)
 [1] "NA"    "NA.1"  "NA.2"  "NA.3"  "NA.4"  "NA.5"  "NA.6"  "NA.7"  "NA.8"  "NA.9"  "NA.10"
[12] "NA.11" "NA.12" "NA.13" "NA.14" "NA.15" "NA.16" "NA.17" "NA.18"
> all(rownames(seqtabAll) %in% samdf$SampleID) # TRUE
[1] FALSE

[benjjneb]

rownames(samdf) <- samdf$SampleIDlib

Might just be a typo? I.e., remove the extraneous "lib" from the end of that line.

[abalter]

Just figured that out! Doh!