Error in if (ncol(m)) { : argument is of length zero

[spatts14]

Hi! I commented on an enhancement in issues as I originally thought it might be an issue of my spatial experiment, however I'm wondering if this is a separate issue.

I tried to convert the spe into a sce object, which worked. However, when I then tired to convert it into an anndata object, I got the error below. This also happened when I tired to go directly from spe --> anndata object. I also tried both writeH5AD and SCE2AnnData, and got the error function for all of them.

It doesn't seem like anything is wrong with me spe object as I can visualize a variety of outputs in R. Apologies in advance if this is a silly question - I am still very new to CS/DS/bioinformatics etc.

# Import data
spe <-readRDS( "path/spe_backup.rds")

# look at spe (SpatialExperiment)
class(spe) 
str(spe)

# Convert spe to sce
sce <- as(spe, "SingleCellExperiment")

# Convert Anndata object
writeH5AD(sce, file = out_path)

# Convert to Anndata object
adata <- SCE2AnnData(sce)

I got an error of the following trying both approaches

ℹ Using the 'counts' assay as the X matrix
Error in if (ncol(m)) { : argument is of length zero

I also tried looking in the source code of both functions to try to see where things were going wrong but I could not figure it out.

Thanks for your help!

[lazappi]

Hi @spatts14

That does seem like something that should be checked. Can you confirm which dataset you are trying here? I wasn't able to work it out from the links you sent in #61. Even better would be if you could share the .rds file you have here if it isn't too big.

Could you also please check what is returned by counts(sce)? It's hard to say without access to the data but my guess is that is empty for some reason.

[spatts14]

Hi @lazappi,

I was trying a dataset in the group, but also tried the dataset that I had shared in #61.
I've checked both the dataset from our group as well as the Bodenmiller dataset. Both are non-empty.

I have also tried to add the .RDS files, but it says it does not support the file type. I am happy to send them via email or some other method that suits you best.

sce <- as(spe, "SingleCellExperiment")

[lazappi]

If you could put them on some kind of file sharing system (Google Drive, OneDrive, Dropbox etc.) and put a link here that would be great.

Or if you could share the minimal code required to go from the raw Bodenmiller data to the object you are testing that would also be helpful (as long as it's not too complex).

[spatts14]

Hi @lazappi

Please let me know if you can't access it
https://drive.google.com/drive/folders/1CuXBWQUPI9hvPxOcl2gmBgHwWRiWo01y?usp=drive_link

[lazappi]

I wasn't able to access it currently. I sent an access request but it might be easier to make it public if there is nothing confidential in the data.

[spatts14]

Apologies, I thought it was public. Should be public now - please let me know if there is any issues.

[lazappi]

Thanks for the data! That was super helpful for working out what the issue was.

I have tracked it down to the colPairs() function in the {SingleCellExperiment} package and have opened an issue there drisso/SingleCellExperiment#73. Depending on how they decide to handle it I may make changes to {zellkonverter}.

In the meantime you can avoid the error but doing something like:

mcols(colPairs(sce)[[1]])$value <- 1

NOTE: This will give you an obsp graph with all the edge weights set to 1 in the file .h5ad file.

[spatts14]

Thanks so much! That worked for us!

Thank you for making the note about the change in edge weights being set to 1.