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liana_wrap error, please help #117

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intawat opened this issue Jun 20, 2023 · 2 comments
Closed

liana_wrap error, please help #117

intawat opened this issue Jun 20, 2023 · 2 comments

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@intawat
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intawat commented Jun 20, 2023

I run the wrapper using mouse ortholog table follow the vignette but got error below (command in bold)

sce <- liana_prep(dat.integrated)

Expression from the RNA assay will be used

Running LIANA with cl_names as labels!

Warning message in exec(output, ...):
“19384 genes and/or 0 cells were removed as they had no counts!”

liana_res <- liana_wrap(sce,
resource = 'custom', # resource has to be set to 'custom' to work with external resources
external_resource = ortholog_resource, # provide orthologous resource
method=c('sca', 'natmi') # run only with sca and natmi for comp. time
)

Running LIANA with label as labels!

Error in map():
ℹ In index: 1.
ℹ With name: custom_resource.
Caused by error in map():
ℹ In index: 1.
Caused by error in h():
! error in evaluating the argument 'x' in selecting a method for function 'rowMeans': size factors should be positive
Traceback:

  1. liana_wrap(sce, resource = "custom", external_resource = ortholog_resource,
    . method = c("sca", "natmi"))
  2. resource %>% map(function(reso) {
    . if (is.null(reso)) {
    . liana_message("Resource was NULL and LIANA's internal methods were run with the Consensus resource",
    . verbose = verbose, output = "warning")
    . reso <- select_resource("Consensus")[[1]]
    . }
    . rlang::invoke(liana_pipe, append(list(sce = sce, op_resource = decomplexify(reso),
    . verbose = verbose, cell.adj = cell.adj, base = base),
    . liana_defaults(...)[["liana_pipe"]]))
    . }) %>% setNames(names(resource))
  3. setNames(., names(resource))
  4. map(., function(reso) {
    . if (is.null(reso)) {
    . liana_message("Resource was NULL and LIANA's internal methods were run with the Consensus resource",
    . verbose = verbose, output = "warning")
    . reso <- select_resource("Consensus")[[1]]
    . }
    . rlang::invoke(liana_pipe, append(list(sce = sce, op_resource = decomplexify(reso),
    . verbose = verbose, cell.adj = cell.adj, base = base),
    . liana_defaults(...)[["liana_pipe"]]))
    . })
  5. map_("list", .x, .f, ..., .progress = .progress)
  6. with_indexed_errors(i = i, names = names, error_call = .purrr_error_call,
    . call_with_cleanup(map_impl, environment(), .type, .progress,
    . n, names, i))
  7. withCallingHandlers(expr, error = function(cnd) {
    . if (i == 0L) {
    . }
    . else {
    . message <- c(i = "In index: {i}.")
    . if (!is.null(names) && !is.na(names[[i]]) && names[[i]] !=
    . "") {
    . name <- names[[i]]
    . message <- c(message, i = "With name: {name}.")
    . }
    . else {
    . name <- NULL
    . }
    . cli::cli_abort(message, location = i, name = name, parent = cnd,
    . call = error_call, class = "purrr_error_indexed")
    . }
    . })
  8. call_with_cleanup(map_impl, environment(), .type, .progress,
    . n, names, i)
  9. .f(.x[[i]], ...)
  10. rlang::invoke(liana_pipe, append(list(sce = sce, op_resource = decomplexify(reso),
    . verbose = verbose, cell.adj = cell.adj, base = base), liana_defaults(...)[["liana_pipe"]]))
  11. .fn(sce = 1, op_resource = 2, verbose = 3, cell.adj = 4,
    . base = 5, test.type = 6, pval.type = 7, assay = 8,
    . assay.type = 9)
  12. get_log2FC(sce, assay.type = assay.type, base)
  13. levels(colLabels(sce)) %>% map(function(subject) {
    . subject_avg <- scater::calculateAverage(subset(sce, select = colLabels(sce) ==
    . subject), assay.type = "normcounts") %>% as_tibble(rownames = "gene") %>%
    . dplyr::rename(subject_avg = value)
    . loso_avg <- scater::calculateAverage(subset(sce, select = !(colLabels(sce) %in%
    . subject)), assay.type = "normcounts") %>% as_tibble(rownames = "gene") %>%
    . dplyr::rename(loso_avg = value)
    . left_join(subject_avg, loso_avg, by = "gene") %>% mutate(avg_log2FC = log2((subject_avg +
    . 1)) - log2((loso_avg + 1))) %>% select(gene, avg_log2FC)
    . }) %>% setNames(levels(colLabels(sce))) %>% enframe(name = "cell") %>%
    . unnest(value)
  14. unnest(., value)
  15. enframe(., name = "cell")
  16. setNames(., levels(colLabels(sce)))
  17. map(., function(subject) {
    . subject_avg <- scater::calculateAverage(subset(sce, select = colLabels(sce) ==
    . subject), assay.type = "normcounts") %>% as_tibble(rownames = "gene") %>%
    . dplyr::rename(subject_avg = value)
    . loso_avg <- scater::calculateAverage(subset(sce, select = !(colLabels(sce) %in%
    . subject)), assay.type = "normcounts") %>% as_tibble(rownames = "gene") %>%
    . dplyr::rename(loso_avg = value)
    . left_join(subject_avg, loso_avg, by = "gene") %>% mutate(avg_log2FC = log2((subject_avg +
    . 1)) - log2((loso_avg + 1))) %>% select(gene, avg_log2FC)
    . })
  18. map_("list", .x, .f, ..., .progress = .progress)
  19. with_indexed_errors(i = i, names = names, error_call = .purrr_error_call,
    . call_with_cleanup(map_impl, environment(), .type, .progress,
    . n, names, i))
  20. withCallingHandlers(expr, error = function(cnd) {
    . if (i == 0L) {
    . }
    . else {
    . message <- c(i = "In index: {i}.")
    . if (!is.null(names) && !is.na(names[[i]]) && names[[i]] !=
    . "") {
    . name <- names[[i]]
    . message <- c(message, i = "With name: {name}.")
    . }
    . else {
    . name <- NULL
    . }
    . cli::cli_abort(message, location = i, name = name, parent = cnd,
    . call = error_call, class = "purrr_error_indexed")
    . }
    . })
  21. call_with_cleanup(map_impl, environment(), .type, .progress,
    . n, names, i)
  22. .f(.x[[i]], ...)
  23. scater::calculateAverage(subset(sce, select = colLabels(sce) ==
    . subject), assay.type = "normcounts") %>% as_tibble(rownames = "gene") %>%
    . dplyr::rename(subject_avg = value)
  24. dplyr::rename(., subject_avg = value)
  25. as_tibble(., rownames = "gene")
  26. scater::calculateAverage(subset(sce, select = colLabels(sce) ==
    . subject), assay.type = "normcounts")
  27. scater::calculateAverage(subset(sce, select = colLabels(sce) ==
    . subject), assay.type = "normcounts")
  28. .local(x, ...)
  29. callNextMethod(x, size.factors = size.factors, ...)
  30. eval(call, callEnv)
  31. eval(call, callEnv)
  32. .nextMethod(x, size.factors = size.factors, ...)
  33. .local(x, ...)
  34. .calculate_average(assay(x, assay.type), ...)
  35. rowMeans(normalizeCounts(x, size.factors, subset.row = subset.row,
    . log = FALSE))
  36. normalizeCounts(x, size.factors, subset.row = subset.row, log = FALSE)
  37. normalizeCounts(x, size.factors, subset.row = subset.row, log = FALSE)
  38. .local(x, ...)
  39. stop("size factors should be positive")
  40. .handleSimpleError(function (cond)
    . .Internal(C_tryCatchHelper(addr, 1L, cond)), "size factors should be positive",
    . base::quote(.local(x, ...)))
  41. h(simpleError(msg, call))
  42. .handleSimpleError(function (cnd)
    . {
    . if (i == 0L) {
    . }
    . else {
    . message <- c(i = "In index: {i}.")
    . if (!is.null(names) && !is.na(names[[i]]) && names[[i]] !=
    . "") {
    . name <- names[[i]]
    . message <- c(message, i = "With name: {name}.")
    . }
    . else {
    . name <- NULL
    . }
    . cli::cli_abort(message, location = i, name = name, parent = cnd,
    . call = error_call, class = "purrr_error_indexed")
    . }
    . }, "error in evaluating the argument 'x' in selecting a method for function 'rowMeans': size factors should be positive",
    . base::quote(h(simpleError(msg, call))))
  43. h(simpleError(msg, call))
  44. cli::cli_abort(message, location = i, name = name, parent = cnd,
    . call = error_call, class = "purrr_error_indexed")
  45. rlang::abort(message, ..., call = call, use_cli_format = TRUE,
    . .frame = .frame)
  46. signal_abort(cnd, .file)
  47. signalCondition(cnd)
  48. (function (cnd)
    . {
    . if (i == 0L) {
    . }
    . else {
    . message <- c(i = "In index: {i}.")
    . if (!is.null(names) && !is.na(names[[i]]) && names[[i]] !=
    . "") {
    . name <- names[[i]]
    . message <- c(message, i = "With name: {name}.")
    . }
    . else {
    . name <- NULL
    . }
    . cli::cli_abort(message, location = i, name = name, parent = cnd,
    . call = error_call, class = "purrr_error_indexed")
    . }
    . })(structure(list(message = c(i = "In index: 1."), trace = structure(list(
    . call = list(IRkernel::main(), kernel$run(), handle_shell(),
    . executor$execute(msg), tryCatch(evaluate(request$content$code,
    . envir = .GlobalEnv, output_handler = oh, stop_on_error = 1L),
    . interrupt = function(cond) {
    . log_debug("Interrupt during execution")
    . interrupted <<- TRUE
    . }, error = .self$handle_error), tryCatchList(expr,
    . classes, parentenv, handlers), tryCatchOne(tryCatchList(expr,
    . names[-nh], parentenv, handlers[-nh]), names[nh],
    . parentenv, handlers[[nh]]), doTryCatch(return(expr),
    . name, parentenv, handler), tryCatchList(expr, names[-nh],
    . parentenv, handlers[-nh]), tryCatchOne(expr, names,
    . parentenv, handlers[[1L]]), doTryCatch(return(expr),
    . name, parentenv, handler), evaluate(request$content$code,
    . envir = .GlobalEnv, output_handler = oh, stop_on_error = 1L),
    . evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
    . debug = debug, last = i == length(out), use_try = stop_on_error !=
    . 2L, keep_warning = keep_warning, keep_message = keep_message,
    . log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,
    . include_timing = include_timing), timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,
    . envir, enclos, user_handlers)), warning = wHandler,
    . error = eHandler, message = mHandler))), handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,
    . envir, enclos, user_handlers)), warning = wHandler,
    . error = eHandler, message = mHandler)), try(f, silent = TRUE),
    . tryCatch(expr, error = function(e) {
    . call <- conditionCall(e)
    . if (!is.null(call)) {
    . if (identical(call[[1L]], quote(doTryCatch)))
    . call <- sys.call(-4L)
    . dcall <- deparse(call, nlines = 1L)
    . prefix <- paste("Error in", dcall, ": ")
    . LONG <- 75L
    . sm <- strsplit(conditionMessage(e), "\n")[[1L]]
    . w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L],
    . type = "w")
    . if (is.na(w))
    . w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
    . type = "b")
    . if (w > LONG)
    . prefix <- paste0(prefix, "\n ")
    . }
    . else prefix <- "Error : "
    . msg <- paste0(prefix, conditionMessage(e), "\n")
    . .Internal(seterrmessage(msg[1L]))
    . if (!silent && isTRUE(getOption("show.error.messages"))) {
    . cat(msg, file = outFile)
    . .Internal(printDeferredWarnings())
    . }
    . invisible(structure(msg, class = "try-error", condition = e))
    . }), tryCatchList(expr, classes, parentenv, handlers),
    . tryCatchOne(expr, names, parentenv, handlers[[1L]]),
    . doTryCatch(return(expr), name, parentenv, handler), withCallingHandlers(withVisible(eval_with_user_handlers(expr,
    . envir, enclos, user_handlers)), warning = wHandler,
    . error = eHandler, message = mHandler), withVisible(eval_with_user_handlers(expr,
    . envir, enclos, user_handlers)), eval_with_user_handlers(expr,
    . envir, enclos, user_handlers), eval(expr, envir,
    . enclos), eval(expr, envir, enclos), liana_wrap(sce,
    . resource = "custom", external_resource = ortholog_resource,
    . method = c("sca", "natmi")), resource %>% map(function(reso) {
    . if (is.null(reso)) {
    . liana_message("Resource was NULL and LIANA's internal methods were run with the Consensus resource",
    . verbose = verbose, output = "warning")
    . reso <- select_resource("Consensus")[[1]]
    . }
    . rlang::invoke(liana_pipe, append(list(sce = sce,
    . op_resource = decomplexify(reso), verbose = verbose,
    . cell.adj = cell.adj, base = base), liana_defaults(...)[["liana_pipe"]]))
    . }) %>% setNames(names(resource)), setNames(., names(resource)),
    . map(., function(reso) {
    . if (is.null(reso)) {
    . liana_message("Resource was NULL and LIANA's internal methods were run with the Consensus resource",
    . verbose = verbose, output = "warning")
    . reso <- select_resource("Consensus")[[1]]
    . }
    . rlang::invoke(liana_pipe, append(list(sce = sce,
    . op_resource = decomplexify(reso), verbose = verbose,
    . cell.adj = cell.adj, base = base), liana_defaults(...)[["liana_pipe"]]))
    . }), map_("list", .x, .f, ..., .progress = .progress),
    . with_indexed_errors(i = i, names = names, error_call = .purrr_error_call,
    . call_with_cleanup(map_impl, environment(), .type,
    . .progress, n, names, i)), withCallingHandlers(expr,
    . error = function(cnd) {
    . if (i == 0L) {
    . }
    . else {
    . message <- c(i = "In index: {i}.")
    . if (!is.null(names) && !is.na(names[[i]]) &&
    . names[[i]] != "") {
    . name <- names[[i]]
    . message <- c(message, i = "With name: {name}.")
    . }
    . else {
    . name <- NULL
    . }
    . cli::cli_abort(message, location = i, name = name,
    . parent = cnd, call = error_call, class = "purrr_error_indexed")
    . }
    . }), call_with_cleanup(map_impl, environment(), .type,
    . .progress, n, names, i), .f(.x[[i]], ...), rlang::invoke(liana_pipe,
    . append(list(sce = sce, op_resource = decomplexify(reso),
    . verbose = verbose, cell.adj = cell.adj, base = base),
    . liana_defaults(...)[["liana_pipe"]])), .fn(sce = 1,
    . op_resource = 2, verbose = 3, cell.adj = 4,
    . base = 5, test.type = 6, pval.type = 7, assay = 8,
    . assay.type = 9), get_log2FC(sce, assay.type = assay.type,
    . base), levels(colLabels(sce)) %>% map(function(subject) {
    . subject_avg <- scater::calculateAverage(subset(sce,
    . select = colLabels(sce) == subject), assay.type = "normcounts") %>%
    . as_tibble(rownames = "gene") %>% dplyr::rename(subject_avg = value)
    . loso_avg <- scater::calculateAverage(subset(sce,
    . select = !(colLabels(sce) %in% subject)), assay.type = "normcounts") %>%
    . as_tibble(rownames = "gene") %>% dplyr::rename(loso_avg = value)
    . left_join(subject_avg, loso_avg, by = "gene") %>%
    . mutate(avg_log2FC = log2((subject_avg + 1)) -
    . log2((loso_avg + 1))) %>% select(gene, avg_log2FC)
    . }) %>% setNames(levels(colLabels(sce))) %>% enframe(name = "cell") %>%
    . unnest(value), unnest(., value), enframe(., name = "cell"),
    . setNames(., levels(colLabels(sce))), map(., function(subject) {
    . subject_avg <- scater::calculateAverage(subset(sce,
    . select = colLabels(sce) == subject), assay.type = "normcounts") %>%
    . as_tibble(rownames = "gene") %>% dplyr::rename(subject_avg = value)
    . loso_avg <- scater::calculateAverage(subset(sce,
    . select = !(colLabels(sce) %in% subject)), assay.type = "normcounts") %>%
    . as_tibble(rownames = "gene") %>% dplyr::rename(loso_avg = value)
    . left_join(subject_avg, loso_avg, by = "gene") %>%
    . mutate(avg_log2FC = log2((subject_avg + 1)) -
    . log2((loso_avg + 1))) %>% select(gene, avg_log2FC)
    . }), map_("list", .x, .f, ..., .progress = .progress),
    . with_indexed_errors(i = i, names = names, error_call = .purrr_error_call,
    . call_with_cleanup(map_impl, environment(), .type,
    . .progress, n, names, i)), withCallingHandlers(expr,
    . error = function(cnd) {
    . if (i == 0L) {
    . }
    . else {
    . message <- c(i = "In index: {i}.")
    . if (!is.null(names) && !is.na(names[[i]]) &&
    . names[[i]] != "") {
    . name <- names[[i]]
    . message <- c(message, i = "With name: {name}.")
    . }
    . else {
    . name <- NULL
    . }
    . cli::cli_abort(message, location = i, name = name,
    . parent = cnd, call = error_call, class = "purrr_error_indexed")
    . }
    . }), call_with_cleanup(map_impl, environment(), .type,
    . .progress, n, names, i), .f(.x[[i]], ...), scater::calculateAverage(subset(sce,
    . select = colLabels(sce) == subject), assay.type = "normcounts") %>%
    . as_tibble(rownames = "gene") %>% dplyr::rename(subject_avg = value),
    . dplyr::rename(., subject_avg = value), as_tibble(., rownames = "gene"),
    . scater::calculateAverage(subset(sce, select = colLabels(sce) ==
    . subject), assay.type = "normcounts"), scater::calculateAverage(subset(sce,
    . select = colLabels(sce) == subject), assay.type = "normcounts"),
    . .local(x, ...), callNextMethod(x, size.factors = size.factors,
    . ...), eval(call, callEnv), eval(call, callEnv), .nextMethod(x,
    . size.factors = size.factors, ...), .local(x, ...),
    . .calculate_average(assay(x, assay.type), ...), rowMeans(normalizeCounts(x,
    . size.factors, subset.row = subset.row, log = FALSE)),
    . normalizeCounts(x, size.factors, subset.row = subset.row,
    . log = FALSE), normalizeCounts(x, size.factors, subset.row = subset.row,
    . log = FALSE), .local(x, ...), stop("size factors should be positive"),
    . .handleSimpleError(<fn>, "size factors should be positive",
    . base::quote(.local(x, ...))), h(simpleError(msg,
    . call)), .handleSimpleError(<fn>, "error in evaluating the argument 'x' in selecting a method for function 'rowMeans': size factors should be positive",
    . base::quote(h(simpleError(msg, call)))), h(simpleError(msg,
    . call)), cli::cli_abort(message, location = i, name = name,
    . parent = cnd, call = error_call, class = "purrr_error_indexed"),
    . rlang::abort(message, ..., call = call, use_cli_format = TRUE,
    . .frame = .frame)), parent = c(0L, 1L, 2L, 3L, 4L,
    . 5L, 6L, 7L, 6L, 9L, 10L, 4L, 12L, 13L, 13L, 15L, 16L, 17L,
    . 18L, 19L, 13L, 13L, 13L, 23L, 24L, 0L, 26L, 0L, 0L, 29L,
    . 30L, 31L, 30L, 30L, 34L, 0L, 36L, 37L, 0L, 0L, 0L, 0L, 42L,
    . 43L, 44L, 43L, 43L, 47L, 0L, 0L, 47L, 47L, 52L, 53L, 54L,
    . 55L, 53L, 57L, 58L, 59L, 59L, 59L, 62L, 63L, 0L, 65L, 0L,
    . 67L, 68L, 69L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE,
    . TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
    . TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
    . TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
    . TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
    . TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
    . TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
    . TRUE, FALSE, FALSE, FALSE, FALSE), namespace = c("IRkernel",
    . NA, "IRkernel", NA, "base", "base", "base", "base", "base",
    . "base", "base", "evaluate", "evaluate", "evaluate", "evaluate",
    . "base", "base", "base", "base", "base", "base", "base", "evaluate",
    . "base", "base", "liana", NA, "stats", "purrr", "purrr", "purrr",
    . "base", "purrr", "liana", "rlang", "liana", "liana", NA,
    . "tidyr", "tibble", "stats", "purrr", "purrr", "purrr", "base",
    . "purrr", "liana", NA, "dplyr", "tibble", "scater", "scater",
    . "scuttle", "methods", "base", "base", "scuttle", "scuttle",
    . "scuttle", "methods", "scuttle", "scuttle", "scuttle", "base",
    . "base", "base", "base", "purrr", "cli", "rlang"), scope = c("::",
    . NA, "local", NA, "::", "local", "local", "local", "local",
    . "local", "local", "::", ":::", "local", "local", "::", "::",
    . "local", "local", "local", "::", "::", ":::", "::", "::",
    . "::", NA, "::", "::", ":::", ":::", "::", ":::", "local",
    . "::", "local", ":::", NA, "::", "::", "::", "::", ":::",
    . ":::", "::", ":::", "local", NA, "::", "::", "::", "::",
    . "local", "::", "::", "::", "local", "local", ":::", "local",
    . "::", "::", "local", "::", "::", "local", "::", "local",
    . "::", "::"), error_frame = c(FALSE, FALSE, FALSE, FALSE,
    . FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
    . FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
    . FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
    . FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
    . FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
    . FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
    . FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
    . FALSE, FALSE, FALSE)), row.names = c(NA, -70L), version = 2L, class = c("rlang_trace",
    . "rlib_trace", "tbl", "data.frame")), parent = structure(list(
    . message = "error in evaluating the argument 'x' in selecting a method for function 'rowMeans': size factors should be positive",
    . call = h(simpleError(msg, call))), class = c("simpleError",
    . "error", "condition")), location = 1L, name = NULL, rlang = list(
    . inherit = TRUE), call = map(., function(subject) {
    . subject_avg <- scater::calculateAverage(subset(sce, select = colLabels(sce) ==
    . subject), assay.type = "normcounts") %>% as_tibble(rownames = "gene") %>%
    . dplyr::rename(subject_avg = value)
    . loso_avg <- scater::calculateAverage(subset(sce, select = !(colLabels(sce) %in%
    . subject)), assay.type = "normcounts") %>% as_tibble(rownames = "gene") %>%
    . dplyr::rename(loso_avg = value)
    . left_join(subject_avg, loso_avg, by = "gene") %>% mutate(avg_log2FC = log2((subject_avg +
    . 1)) - log2((loso_avg + 1))) %>% select(gene, avg_log2FC)
    . }), use_cli_format = TRUE), class = c("purrr_error_indexed",
    . "rlang_error", "error", "condition")))
  49. cli::cli_abort(message, location = i, name = name, parent = cnd,
    . call = error_call, class = "purrr_error_indexed")
  50. rlang::abort(message, ..., call = call, use_cli_format = TRUE,
    . .frame = .frame)
  51. signal_abort(cnd, .file)
@dbdimitrov
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Hi @intawat,

I assume you have are encountering some kind of an issue with the counts that you are using - you should use log-normalized. Specifically, I see that liana has filtered 19384 genes which means that something is wrong, and likely you simply have none left. Check if you are not using the residuals or any type of negative values from your integration approach.

@intawat
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intawat commented Jun 21, 2023 via email

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@intawat @dbdimitrov