What does gene-level summarization mean in FastBMD?

Microarray data provides probe-level expression measurements and RNA-seq data provides exon-level or transcript-level (i.e. different isoforms of the same gene) expression measurements. However, current functional annotations are mainly assigned 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. In particular,

  • Averages / medians of multiple probe intensities (microarray)
  • Sums of counts from multiple transcripts (RNAseq)