addGeneExpressionMatrix Error

[jinoh-neuro]

Hi,

I am trying to add a paired scRNA dataset (in the form of a RangedSummarizedExperiment) from a 10X Multiome Experiment to my ArchR Project. However, I get the following error:

ArchR logging to : ArchRLogs/ArchR-addGeneExpressionMatrix-14cfc4f9fad94-Date-2021-10-19_Time-17-52-25.log If there is an issue, please report to github with logFile! 2021-10-19 17:52:27 : Overlap w/ scATAC = 0.981 2021-10-19 17:52:27 : Overlap Per Sample w/ scATAC : atac=5149 Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘NSBS’ for signature ‘"CompressedIntegerList"’

Wondering how this error may be fixed. Thank you!

ArchR-addGeneExpressionMatrix-14cfc4f9fad94-Date-2021-10-19_Time-17-52-25.log

[jinoh-neuro]

For reference, the code I used was

projE13Multi <- addGeneExpressionMatrix(input = projE13Multi, seRNA = seRNA, force = TRUE)

where projE13Multi is the name of my ArchRProject

[rcorces]

I dont have enough information to help.

1) Are you able to execute the multiome tutorial without issue? https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Multiome.html 2) How did you create your seRNA object

[jinoh-neuro]

Hi, thanks for the quick response!

To answer your questions:

1. Yes, the multiome tutorial works fine

2. seRNA was created by first creating a "SingleCellExperiment" object with DropletUtils read10xCounts function that utilizes the feature matrix, barcodes, and rna features sce <- read10xCounts(samples = "path/to/samples", sample.names = names(samples), col.names = TRUE, type = "auto", version = "3", genome = NULL)

I then appended the name to cellNames for matching colnames(sce) <- paste("sampleName", colnames(sce), sep = "#")

SingleCellExperiment object was then converted to RangedSummarizedExperiment with seRNA <- as(sce, "RangedSummarizedExperiment")

I had to create the seRNA object in this method, because the .h5 matrix was not available to me, so I was unable to use the import10xFeatureMatrix function

[rcorces]

I imagine there is something off about your seRNA object. It isnt obvious from the log file - it looks pretty equivalent to the expected. One possibility is that the gene names listed in your seRNA object do not align with the gene names in your ArchR gene annotation.

[jinoh-neuro]

I see, thank you! I will play around with modifying the seRNA object gene names. Is there a way I can view the ArchR gene annotations/how they are annotated?

[rcorces]

https://www.archrproject.com/reference/getGeneAnnotation.html

[jinoh-neuro]

Thank you

[jinoh-neuro]

Hi, from the tutorial I understand how to attach a custom genome annotation when creating an arrow file, but how may I attach a custom gene annotation?

[rcorces]

this is described in the manual - https://www.archrproject.com/bookdown/getting-set-up.html

[jinoh-neuro]

Hi, thank you for the help. I have resolved this issue by converting the ArchR geneannotation to ENSEMBL

[aa20g217]

@jinoh-neuro Could you please explain how you solved it?