Microarray data provides probe-level expression measurements, while RNA-seq data provides expression at exon-level or transcript-level (i.e. different isoforms of the same gene) expression measurements. However, current functional annotations are assigned at the gene level. It is necessary to first map the probe-level or transcript-level measurements to the corresponding gene-level measurements.
When multiple probes or transcripts are mapped to the same gene, they need to be summarized into a single value for the corresponding gene. In miRNet, the averages of multiple probe intensities (microarray/QPCR), or sums of counts from multiple transcripts (RNAseq) are used to perform gene-level summarization.