Error in PLIER while performing pseudobulk analysis with single-cell data (Error in svd(Y) : infinite or missing values in 'x')

[recervictory]

Hello,

I am attempting to use the PLIER package for pseudobulk analysis of single-cell RNA sequencing data. I have generated pseudobulk data using the PseudobulkExpression function from Seurat and passed it to the PLIER function. However, I encounter an error during the SVD computation:

`
pseudobulk_data <- PseudobulkExpression(
object = seuratObject,
group.by = c("sample", "cell_type"), # Grouping by sample and cell type
assays = "RNA", # Assay to use
features = NULL, # Use all features
method = "average", # Aggregation method
normalization.method = "LogNormalize",# Normalization method
scale.factor = 10000, # Scale factor for normalization
verbose = TRUE, # Print progress
layer = "data"
)

plierResult <- PLIER(pseudobulk_data, allPaths)

ERROR
Selecting common genes: 6078
Removing 12 pathways with too few genes
Computing SVD
Error in svd(Y) : infinite or missing values in 'x'

`

[wgmao]

Could you check if there are any NA or infinite values in pseudobulk_data? If the data looks good, the issues might be due to some genes having constant values (e.g., all zeros) across all cells. By default, PLIER applies the z-score transformation on genes, which can result in constant gens being converted to NA values.