[Microarray] Issue combining dataframes using bind_rows() when getBM() returns no results

[cyouh95]

Description

The following error occurred when rendering Affymetrix.qmd for one dataset (but same issue could potentially arise in Agile1CMP.qmd too):

Error in `dplyr::bind_rows()`:
  ! Can't combine `..1$ensembl_gene_id` <logical> and `..2$ensembl_gene_id` <character>.

Error occurs when getBM() returns no rows, then ensembl_gene_id column is assumed to be logical type, causing the incompatibility in bind_rows().

GeneLab_Data_Processing/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/workflow_code/bin/Affymetrix.qmd

Lines 636 to 652 in 90d6bb5

	df_mapping <- data.frame()
	for (i in seq_along(probe_id_chunks)) {
	probe_id_chunk <- probe_id_chunks[[i]]
	print(glue::glue("Running biomart query chunk {i} of {length(probe_id_chunks)}. Total probes IDS in query ({length(probe_id_chunk)})"))
	message(glue::glue("Running biomart query chunk {i} of {length(probe_id_chunks)}. Total probes IDS in query ({length(probe_id_chunk)})")) # NON_DPPD
	chunk_results <- biomaRt::getBM(
	attributes = c(
	expected_attribute_name,
	"ensembl_gene_id"
	),
	filters = expected_attribute_name,
	values = probe_id_chunk,
	mart = ensembl)
	df_mapping <- df_mapping %>% dplyr::bind_rows(chunk_results)
	Sys.sleep(10) # Slight break between requests to prevent back-to-back requests
	}

Solution

Check if chunk_results contains any rows before binding to df_mapping in Affymetrix.qmd / Agile1CMP.qmd:

if (nrow(chunk_results) > 0) {
    df_mapping <- df_mapping %>% dplyr::bind_rows(chunk_results)
}