Warning:The assays in your SummarizedExperiment have row names, but they don't agree with the row names of the SummarizedExperiment object itself

[artur-sannikov]

Reposting from Slack.

When creating a new column in a tse object, I get Warning: tidySummarizedExperiment says: the assays in your SummarizedExperiment have row names, but they don't agree with the row names of the SummarizedExperiment object itself. It is strongly recommended to make the assays consistent, to avoid erroneous matching of features.

For example, running

animal_tse <-
  tse |>
  mutate(animal_id = substr(sample_name, 1, 10))

get me Error: 67 specified rows can't be found. I have 67 species in rowData. I confirmed that the rownames of the assay and the tse object itself are identical/

I was not able to reproduce the issue on the test pasilla data.

@HelenaLC suggested running

. <- lapply(assays(tse, withDimnames=FALSE), rownames)
sapply(.[-1], identical, .[[1]])

That gave me

sapply(.[-1], identical, .[[1]])
#> named list()

sapply(., identical, rownames(tse))
#> counts 
 FALSE 

The code that checks for warning is here.

If I run if checks individually, they all give me TRUE, thus the warning.

@HelenaLC said that

If they are all TRUE, I guess the problematic line is all(rownames(assays(se, withDimnames = FALSE)[[1]]) %in% rownames(se)) ... in your original post, you did not specify withDimnames , so this went unnoticed. withDimnames=TRUE (default) will basically set these on the fly, so they always appear to match. Simply overwriting the assay might fix it, e.g., assay(tsne) <- assay(tsne) (since the accessor sets the row names according to rownames(tsne)) ...but I'm not sure

So, doing

assay(tse) <- assay(tse)

solved the problem.

[stemangiola]

tagging @csoneson, for interest, as she worked previously on this matter.