dim(X) must have a positive length

[TommySchooner]

Hi there,

Thank you very much for helping! This is the first time for me to use sleuth and R language.

After I have generated the tsv files from Kallisto, I tried to run them in sleuth. I have done the following:

library(sleuth) base_dir <- "~/Desktop/Final_Project/3_Sp100_Data_analysis/Sp100_single_ended_Kallisto_expression_results" s2c <- read.table(file.path("~/Desktop/Final_Project/3_Sp100_Data_analysis/Sp100_single_ended_Kallisto_expression_results", "Kallisto_info.txt"), header = TRUE, stringsAsFactors=FALSE) sample_id <- c("IFN6h_kallisto", "Mock_kallisto") kal_dirs <- sapply(sample_id, function(id)file.path(base_dir,id)) s2c <- dplyr::select(s2c, sample=sample, condition) s2c <- dplyr::mutate(s2c, path=kal_dirs)

However, the error appears. I wonder what have I done wrong?

dropping unused factor levels .. normalizing est_counts 1 targets passed the filter normalizing tpm merging in metadata summarizing bootstraps ..Sample 'IFN6h_kallisto' had this error message: Error in apply(bs_mat, 2, quantile) : dim(X) must have a positive length Sample 'Mock_kallisto' had this error message: Error in apply(bs_mat, 2, quantile) : dim(X) must have a positive length

sleuth_prep(s2c, extra_bootstrap_summary = TRUE) でエラー: At least one core from mclapply had an error. See the above error message(s) for more details. 此外: 警告メッセージ: parallel::mclapply(x, y, mc.cores = num_cores) で: all scheduled cores encountered errors in user code

I have the s2c:

sample condition 1 IFN6h_kallisto IFN-treated 2 Mock_kallisto mock

path 1 ~/Desktop/Final_Project/3_Sp100_Data_analysis/Sp100_single_ended_Kallisto_expression_results/IFN6h_kallisto 2 ~/Desktop/Final_Project/3_Sp100_Data_analysis/Sp100_single_ended_Kallisto_expression_results/Mock_kallisto

Thank you very much for helping!

Best regards,

Oscar