What does gene-level summarization mean?

Microarray data provides probe-level expression measurements and RNA-seq data provides transcript-level (i.e. different isoforms of the same gene) expression measurements. However, current functional annotations and analysis are mainly performed at the gene or protein level.

Therefore, when multiple probes or transcripts are mapped to the same gene, they need to be summarized into a single value for that gene. At the Gene Annotation step, users can choose to use the averages or medians of multiple probe intensities (microarray), or sums of counts from multiple transcripts (RNA-seq) to perform gene-level summarization.