[Bug] error while generating expression

[FloresKneil]

I run the App locally via RStudio, the window crashes, the console freezes and when I look into the log file I get:

reading in files with read_tsv
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 
transcripts missing from tx2gene: 213079
summarizing abundance
summarizing counts
summarizing length
summarizing inferential replicates
Warning: Error in colnames<-: attempt to set 'colnames' on an object with less than two dimensions

my input files are kallisto counts computed via command line (abundance.h5)

My metadata and transcript mapping files are: CSVs.zip

Additional context Add any other context about the problem here.

[wyguo]

Hi, The formats of your input files are not correct. (1) The transcript-gene assocation table, the first line should be column names, e.g. TXNAME and GENEID. (2) You metadata table doesn't have a column to distinguish the biological replicates. If your data has no replicates, 3D App won't work. And please remove space or sepecial symbols in your condition column. It may cause troubles. You can check the user manual for how to preprare the input files: https://github.com/wyguo/ThreeDRNAseq/blob/master/vignettes/user_manuals/3D_RNA-seq_App_manual.md#input-files