Table 1.

Notations

Notation	Description
T	set of transcripts in a gene; Ti denotes the ith transcript of the gene
l	lengths of transcripts; li denotes the length of transcript Ti
r	set of reads aligned to a gene; rj is the jth read aligned to the gene
P	the probability of a read generated by the transcripts in the gene,
	specifically, P=$[p_1,p_2,\dots ,p_{\left|\mathit{T}\right|}]$
$\tilde{\mathit{l}}$	the effective lengths of the transcripts, where ${\tilde{l}}_i=l_i-l_r+1$,
	li and lr are the length of Ti and the length of the read respectively
qij	read sampling probability, $q_{\mathit{ij}}=\frac{1}{{\tilde{l}}_i}$ if read rj is aligned to Ti,
	otherwise qij = 0
E	the transcripts’ expressions in NanoString or Exon-array platform
aij	a soft assignment of read rj to transcript Ti in the EM algorithm
α	a scaling factor between the transcript expressions in different platforms
λ	hyper-parameter