so <- sleuth_prep(s2c, ~genotype_variation_s, extra_bootstrap_summary = TRUE,
read_bootstrap_tpm=TRUE)
reading in kallisto results
dropping unused factor levels
.....
normalizing est_counts
Error in if (sum(filter_bool) == 0) { :
missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In check_num_cores(num_cores) :
It appears that you are running Sleuth from within Rstudio.
Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
Hello, dear friends! Help me please, i dont understand why Sleuth output that result :(
sample_id <- dir(file.path("~/Desktop/xxxxx/kallisto_output" )) sample_id
kal_dirs <- file.path("~/Desktop/xxxxx/kallisto_output", sample_id, "kallisto") kal_dirs
s2c <- read.table(file.path("~/Desktop/xxxxx/metadata/meta(copy).tsv"), header = TRUE, stringsAsFactors = FALSE, sep = " ")
s2c <- dplyr::select(s2c, sample = sample_id, genotype_variation_s) s2c <- dplyr::mutate(s2c, path = kal_dirs)
s2c$genotype_variation_s <- as.factor(s2c$genotype_variation_s) s2c$genotype_variation_s <- relevel(s2c$genotype_variation_s, ref = "c-like")
so <- sleuth_prep(s2c, ~genotype_variation_s, extra_bootstrap_summary = TRUE, read_bootstrap_tpm=TRUE)
reading in kallisto results dropping unused factor levels ..... normalizing est_counts Error in if (sum(filter_bool) == 0) { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In check_num_cores(num_cores) : It appears that you are running Sleuth from within Rstudio. Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1. If you wish to take advantage of multiple cores, please consider running sleuth from the command line.