Bulk gene expression matrix format

[dlubawska]

Apologies for perhaps a silly question - an undergrad here! :)
Regarding the Y input file - should I use TPM or read count expression matrix? I've obtained both of those after pre-processing raw RNAseq reads with Trimmomatic & applying Kallisto for gene expression quantification (using the quanTIseq pipeline).

Y: a Ngene by Nsample matrix contains bulk gene expression data. This should be in linear-scale data without log-transformation.

Thank you in advance!