Sample of a Co-op Experience: microarray probe set filtering and globin depletion in RNA-Seq data

Science Co-op brought me to work at the PROOF (Prevention of Organ Failure) Centre of Excellence at St. Paul's Hospital, where I mostly performed exploratory assessments of various genomic expression measurement platforms. I will discuss two projects I was involved in. The first is a part of PROOF's computational pipeline of biomarker discovery: probe set filtering. Here, probe sets filtered by a new method, PVAC, are assessed for their resulting signal in comparison to a more established method, FARMS. The second project compares two samples from each of six healthy subjects for their gene expressions from a RNA-Seq assay. We compare samples depleted of globins with non-depleted ones to assess the efficacy of globin depletion on the detection of other gene transcripts.