Use the immuneResponseRNA plugin to quantify gene expression levels for the Oncomine™ Immune Response Research Assay. This plugin produces gene transcript quantification from sequence read data. The Run Summary screen includes gene expression counts (number of aligned reads to a given gene target), a data analysis summary, and QC plots. The normalized, gene-level count data from the run are available to download for further analyses with Affymetrix™ Transcriptome Analysis Console (TAC) 3.1 software.

The immuneResponseRNA plugin requires a Target Regions BED file and an associated Reference Library FASTA file. See Reference Management for more information on installing these files.

The plugin also accepts a second—optional—BED file that specifies a subset of target genes allowing sample clustering.