Error in validate_infercnv_obj(infercnv_obj): Problem detected w/ infercnv_obj and Error: No feature overlap between existing object and new layer data

[Prakrithi-P]

Hi when I run inferCNV I get errors, irrespective of the versions.

In an older Version

options("CY112sn_subset.assay.version" = "v3")
infercnv_obj = CreateInfercnvObject(
raw_counts_matrix=GetAssayData(CY112sn_subset, slot="scale.data"),
annotations_file=infercnv_meta,
delim="\t",
gene_order_file="infercnv//hg38_gencode_v27.txt",
ref_group_names=c("CD8+ T cell","B cell","CD4+ T cell","Lymphatic endothelial cell","Fibroblast","Endothelial cell"))
#Macrophage

out_dir = tempfile()
infercnv_obj_default = infercnv::run(
infercnv_obj,
cutoff=1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
out_dir="./infercnv/CY112/",
cluster_by_groups=TRUE,
plot_steps=FALSE,
denoise=TRUE,
HMM=FALSE,
no_prelim_plot=TRUE,
png_res=60
)

This gave me the following error:
INFO [2024-04-18 17:56:52] define_signif_tumor_subclusters(p_val=0.1
INFO [2024-04-18 17:56:52] define_signif_tumor_subclusters(), tumor: CD8+ T cell
INFO [2024-04-18 17:56:52] Less cells in group CD8+ T cell than k_nn setting. Keeping as a single subcluster.
INFO [2024-04-18 17:56:52] define_signif_tumor_subclusters(), tumor: B cell
INFO [2024-04-18 17:56:52] Less cells in group B cell than k_nn setting. Keeping as a single subcluster.
INFO [2024-04-18 17:56:52] define_signif_tumor_subclusters(), tumor: Macrophage
Warning message:
“Data is of class matrix. Coercing to dgCMatrix.”
Error: No feature overlap between existing object and new layer data
Traceback:

1. infercnv::run(infercnv_obj, cutoff = 1, out_dir = "./infercnv/CY112/",
   . cluster_by_groups = TRUE, plot_steps = FALSE, denoise = TRUE,
   . HMM = FALSE, no_prelim_plot = TRUE, png_res = 60)
2. define_signif_tumor_subclusters(infercnv_obj = infercnv_obj,
   . p_val = tumor_subcluster_pval, k_nn = k_nn, leiden_resolution = leiden_resolution,
   . leiden_method = leiden_method, leiden_function = leiden_function,
   . hclust_method = hclust_method, cluster_by_groups = cluster_by_groups,
   . partition_method = tumor_subcluster_partition_method, per_chr_hmm_subclusters = per_chr_hmm_subclusters,
   . z_score_filter = z_score_filter)
3. .single_tumor_leiden_subclustering(tumor_group = tumor_group,
   . tumor_group_idx = tumor_group_idx, tumor_expr_data = tumor_expr_data,
   . chrs = chrs, k_nn = k_nn, leiden_resolution = leiden_resolution,
   . leiden_method = leiden_method, leiden_function = leiden_function,
   . hclust_method = hclust_method)
4. .leiden_seurat_preprocess_routine(expr_data = tumor_expr_data,
   . k_nn = k_nn, resolution_parameter = leiden_resolution, objective_function = leiden_function)
5. CreateSeuratObject(expr_data, assay = "infercnv", project = "infercnv",
   . names.field = 1)
6. CreateSeuratObject.default(expr_data, assay = "infercnv", project = "infercnv",
   . names.field = 1)
7. CreateAssay5Object(counts = counts, min.cells = min.cells, min.features = min.features,
   . ...)
8. .CreateStdAssay(counts = counts, min.cells = min.cells, min.features = min.features,
   . transpose = transpose, type = type, csum = csum, fsum = fsum,
   . ...)
9. .CreateStdAssay.list(counts = counts, min.cells = min.cells,
   . min.features = min.features, transpose = transpose, type = type,
   . csum = csum, fsum = fsum, ...)
10. LayerData<-(object = *tmp*, layer = layer, features = features[[layer]],
    . cells = cells[[layer]], transpose = transpose, value = counts[[layer]])
11. LayerData<-.Assay5(object = *tmp*, layer = layer, features = features[[layer]],
    . cells = cells[[layer]], transpose = transpose, value = counts[[layer]])
12. stop("No feature overlap between existing object and new layer data",
    . call. = FALSE)

In the New version 1.19.1, the same command gives the following error:
INFO [2024-04-23 18:08:51] ::above_min_mean_expr_cutoff:Start
INFO [2024-04-23 18:08:51] Removing 1919 genes from matrix as below mean expr threshold: 1
INFO [2024-04-23 18:08:51] validating infercnv_obj
ERROR [2024-04-23 18:08:51] hmm.... rownames([email protected] != rownames(infercnv_obj@gene_order))
Error in validate_infercnv_obj(infercnv_obj): Problem detected w/ infercnv_obj
Traceback:

1. infercnv::run(infercnv_obj, cutoff = 1, out_dir = "./infercnv/CY128/",
   . cluster_by_groups = TRUE, plot_steps = FALSE, denoise = TRUE,
   . HMM = FALSE, no_prelim_plot = TRUE, png_res = 60)
2. require_above_min_mean_expr_cutoff(infercnv_obj, cutoff)
3. remove_genes(infercnv_obj, indices)
4. validate_infercnv_obj(infercnv_obj)
5. stop("Problem detected w/ infercnv_obj")

I get the same errors despite the rownames being the same. Could you please help me solve this?

Thanks,
Prakrithi