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)
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.
The commands used: