Seurat v5 SCTransform warning messages (I consistently get 50 warnings)

Question

[michelle.swarovski]

# After creating a merged seurat object using this code:

OVLT_merged <- merge(M_OVLT_Saline, y = c(M_OVLT_LPS, M_OVLT_PolyIC, F_OVLT_Saline, F_OVLT_LPS, F_OVLT_PolyIC), add.cell.ids = c("M_OVLT_Saline", "M_OVLT_LPS", "M_OVLT_PolyIC", "F_OVLT_Saline", "F_OVLT_LPS", "F_OVLT_PolyIC"), project = "OVLT")

# I then added the percent mitochondrial and RBC genes to the object,

OVLT_merged <- PercentageFeatureSet(OVLT_merged , pattern = "^mt-", col.name = "MT")
OVLT_merged <- PercentageFeatureSet(OVLT_merged , pattern = "^Hba", col.name = "RBC")
OVLT_merged <- PercentageFeatureSet(OVLT_merged , pattern = "^Hbb", col.name = "RBC")

# So I then could filter the data using:

OVLT_filtered <- subset(OVLT_merged, subset = RBC < 0.01 & MT < 5 & nFeature_RNA < 6000 & nFeature_RNA > 300)

# Which I then ran SCTransform v2 to normalize the data:

OVLT <- SCTransform(OVLT_filtered, vars.to.regress=c("MT","RBC"), vst.flavor = "v2", return.only.var.genes = FALSE, verbose = FALSE)

In return, I get 50 warning messages the first of which is specified below:

1: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE. Error in cat("1: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE.", : argument 2 (type 'S4') cannot be handled by 'cat'

Does anyone know what maybe going wrong?

Thank you so much!

Michelle

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or use one of (a) the option highlighted in the image below/ (b) fenced code blocks for multi-line code. Fenced code blocks are useful in syntax highlighting. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.

[fracarb8]

Nothing to worry about. Seurat v5 release has introduced several versioning issues.