Phyloseq sample data error: non-zero dimensions?
I'm trying to filter/extract out individuals from the genetic data that has a gut gene data.
Got an Error message saying that my Phyloseq object (sample_data) is zero dimension but when I looked at the gut_phyloseq object attribute, it said Name: sam_data Type: list[128x185] (phyloseq::sample_data) Value: A data.frame with 128 and 185 columns
Where is the problem and why is it saying that my phyloseq sample_data object is zero-dimension?
Full code of what I was working on:
# Get SampleID from the host genetic data
dis_mtx_file <- "plinkdismtx.gut.mdist.id"
dis_mtx <- read.table(dis_mtx_file, header = FALSE, stringsAsFactors = FALSE)
sample_ids_with_dis <- dis_mtx$V1
# Filter out individuals data who also have the gut data, then we extract those gut data out.
gut_phyloseq <- readRDS('gut_phyloseq.rds')
filt_physeq <- subset_samples(gut_phyloseq, sample_names(gut_phyloseq) %in% sample_ids_with_dis)
> Error in validObject(.Object) :
invalid class “sample_data” object: Sample Data must have non-zero dimensions.
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Chris Dean •
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Emily •
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Emily •
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DESeq confusing results
written by leranwangcs •
I think it would be helpful to reformat the structure of your post. It is difficult to read and unclear what your question is.
Edited the post. I dont understand why R is saying my sample_data object for phyloseq is zero-dimension when it shouldn't be but not sure where I made the mistake to get that error.
You are likely receiving this error because this expression does not evaluate to TRUE:
In other words, none of the sample names returned by
sample_names()match any of the sample names insample_ids_with_dis. You can verify this by running the following:If this evaluates to FALSE, then I would recommend inspecting the content of these two objects to diagnose the issue.