I have run Kallisto on my samples to try and get transcript-level intensities. I now want to do a transcript-level expression analysis using the
catchKallisto command from the
This went quite well.
library(edgeR) paths <- list.files(path = "kallisto/output/", pattern="Sample", full.names=TRUE) data <- catchKallisto(paths = paths, verbose = TRUE )
But the resulted list$counts are not counts (Are these TPMs???).
kallisto/output//L75442_Track-118107 Y110A7A.10.1 1.439992e+03 Y110A7A.10.2 8.353787e-03 F27C8.1.1 1.200000e+01 F27C8.1.2 0.000000e+00 F07C3.7 5.300000e+01 kallisto/output//L75443_Track-118108 Y110A7A.10.1 1575.499243 Y110A7A.10.2 1.500757 F27C8.1.1 0.000000 F27C8.1.2 11.000000 F07C3.7 52.000000 kallisto/output//L75444_Track-118109 Y110A7A.10.1 1.546000e+03 Y110A7A.10.2 1.515167e-04 F27C8.1.1 5.000000e+00 F27C8.1.2 0.000000e+00 F07C3.7 7.000000e+01
Do I need to change them into counts (just by rounding them) or is it ok for
edgeR to have them as such?