Warning messages and no Dimnames with Nanostring FFPE NSCLC CosMx Data Set

[Rayan21100]

Hello everyone !

I'm trying to load the Nanostring FFPE NSCLC CosMx Data Set as a Seurat Object in R and trying to follow the vignette on this dataset (https://satijalab.org/seurat/articles/seurat5_spatial_vignette_2#human-lung-nanostring-cosmx-spatial-molecular-imager).

I used the LoadNanostring function as in the vignette :

nano.obj <- LoadNanostring(data.dir = "/brahms/hartmana/vignette_data/nanostring/lung5_rep1", fov = "lung5.rep1")

I have two problems :

• First I have two warning messages:

Warning messages:
1: In Polygon(coords = cx) : less than 4 coordinates in polygon
2: In Polygon(coords = cx) : less than 4 coordinates in polygon

I don't really know what it means and if it's really a problem

• Then, when my Seurat object is created, my count matrix doesn't have any row/column name as you can see in the picture. This dataset is divided into FOVs and for each FOVs the cell IDs start again from 1, do you think the absence of cell names in the count matrix could be linked to this ?

For the absence of gene name it is really weird, in "molecules" I can find the list of all the genes as you can see in the picture below (AATK, ABL1, ABL2 etc...). Why is this list recognized under molecules and not as the row names of the count matrix ?

As the download link for the cell boundaries in the vignette is not working anymore, I asked Nanostring for them, so maybe the problem is from the file they gave me ? I can send the head of each csv file I have if needed,

EDIT :

I also tried the method found here: #6786 with :

data <- ReadNanostring(data.dir = data.dir, type = "centroids")<br>
cents <- CreateCentroids(data$centroids)
coords <- CreateFOV(coords = list("centroids" = cents), type = "centroids")
obj <- CreateSeuratObject(counts = data$matrix)
obj[["fov"]]<-subset(coords, cell=Cells(obj))

The data object created with ReadNanostring works really well and I have indeed the rows/columns names of the count matrix, but when I use CreateSeuratObject the Seurat Object created also looses the rows/columns names

Thank you in advance for your help !