I am working on pathway analysis using GAGE and Pathview. I can determine up-regulated and down-regulated pathways and get corresponding heatmaps, but I have a question on the "type" of counts I should be using. When I did differential gene expression analysis I generated a DGElist that has pseudo.counts which if I understand correctly are transformed and normalized. I also have a Counts Per Million list that was generated after quality filtering of raw counts. I get similar differentially regulated pathways while using either counts but I do not know which one is more appropriate to use. If anyone can help me I would very much appreciate the help. Thanks!
-
NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM -
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM
Comment