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pull_gse65682.R

@@ -111,7 +111,7 @@ gse65682_feature_metadata <- anno_u219 |>
     ungroup() |>
     mutate(across(c(ENSEMBL, UNIPROT), ~ na_if(.x, ""))) |>
     rename(feature_id = PROBEID) |>
-    right_join(tibble(feature_id = your_probes_mars), by = "PROBEID") # guarantee every probe gets a row
+    right_join(tibble(feature_id = your_probes_mars), by = "feature_id")
 
 stopifnot(nrow(gse65682_feature_metadata) == length(your_probes_mars))
 stopifnot(!any(duplicated(gse65682_feature_metadata$feature_id)))
@@ -124,7 +124,7 @@ gse65682_expr_long <- as_tibble(exprs(gset), rownames = "feature_id") |>
 
 stopifnot(nrow(gse65682_expr_long) == nrow(exprs(gset)) * ncol(exprs(gset)))
 stopifnot(all(unique(gse65682_expr_long$sample_id) %in% gse65682_metadata$sample_id))
-stopifnot(all(unique(gse65682_expr_long$PROBEID) %in% gse65682_feature_metadata$PROBEID))
+stopifnot(all(unique(gse65682_expr_long$feature_id) %in% gse65682_feature_metadata$feature_id))
 
 stopifnot(!any(duplicated(gse65682_metadata$sample_id)))
 stopifnot(nrow(gse65682_metadata) == 802)