I am working on differential expression benchmarking and I use tximport to read in the data from Salmon/Sailfish/Kallisto/RSEM.
Sample data is always the same, only different quantification or alignments tools are used. Everything besides abundances.h5 import works fine. I do have rhdf5 library installed and running. I can read in the data from Kallisto's TSV files, but when I try to do the same with .h5 I get:
Error: all(c(lengthCol, abundanceCol) %in% names(raw)) is not TRUE
Is there any reason why it wouldnt work with h5 files? Any way around this? Thanks!