Hello, I am using StandR to analyze my GeoMx data. I load my data by running:

library(standR)
library(SpatialExperiment)
library(limma)
library(ExperimentHub)
library(ggplot2)

library(tidyverse)

countFile <- read_tsv("TargetCount.txt") %>% as.data.frame()
sampleAnnoFile <- read_tsv("SampleAnno.txt") %>% as.data.frame()
featureAnnoFile <- read_tsv("featureAnno.txt") %>% as.data.frame()
# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

Then I import the data into a spatial experiment object by running:

spe <- readGeoMx(countFile, sampleAnnoFile, featureAnnoFile)

But I got this error:

Error in SummarizedExperiment(...) : 
  the rownames and colnames of the supplied assay(s) must be NULL or identical to those of the SummarizedExperiment object
  (or derivative) to construct

I would be very appreciated it if someone could give me an idea of what may have gone wrong. Many thanks!

This points to a mismatch between

1. the rownames of countFile and rownames of featureAnnoFile (row metadata) and/or
2. the colnames of countFile and rownames of sampleAnnoFile (column metadata)

As the error suggest, one of them needs to be NULL (e.g., when the counts don't have row/colnames, the rownames of the corresponding metadata are used), or both need to match.

Here's an example...

# mock matrix with column names only
cs <- letters[1:20]
y <- matrix(0, 10, length(cs),
    dimnames = list(NULL, cs))

# assay colnames and colData rownames match
cd <- data.frame(x = seq_along(cs), row.names = cs)
SummarizedExperiment(list(y), colData = cd) # valid

# rownames missing from colData, assay colnames are used
cd <- data.frame(x = seq_along(cs), row.names = NULL)
SummarizedExperiment(list(y), colData = cd) # valid

# mismatch gives error
cd <- data.frame(x = seq_along(cs), row.names = sample(cs))
SummarizedExperiment(list(y), colData = cd) # error!
> Error in SummarizedExperiment(list(y), colData = cd) : 
  the colnames of the supplied assay(s) must be NULL
  or identical to those of the SummarizedExperiment
  object (or derivative) to construct