Issue with simpleLoess #278
Description
Hello!
I am enjoyed on the abilities the sleuth provides on RNA-Seq data analysis. So I try to use it in my current project. I have a large dataset, where from I am interested in looking the DE for 15 genes (which corresponds to 224 DE transcripts previously identified by lrt analysis. I ran an analysis again, with gene aggregation, target mapping and filtering by a vector containing the 224 transcript ids.
In sleuth_prep(s2c, num_cores = max(1L, parallel::detectCores() - : 325270 target_ids are missing annotations for the aggregation_column: gene. These target_ids will be dropped from the gene-level analysis. If you did not expect this, check your 'target_mapping' table for missing values. fitting measurement error models shrinkage estimation Error in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, : invalid 'x' Calls: sleuth_fit -> shrink_df -> eval -> loess -> simpleLoess Execution halted The commands used:
t2g <- read.csv('DEG_vs_comb_prot_dedup.map.tsv', sep="\t", stringsAsFactors = FALSE) head(t2g) filter_id <- t2g$target_id[t2g$gene != ''] so <- sleuth_prep(s2c, num_cores = max(1L, parallel::detectCores() - 10L), extra_bootstrap_summary = TRUE, read_bootstrap_tpm = TRUE, target_mapping = t2g, aggregation_column = "gene", gene_mode = TRUE, filter_target_id = filter_id, max_bootstrap = 500)