One of the goals of RNA-seq is to detect differential gene/transcripts expression (for the sake of simplicity, we use the term "gene" to represent gene or transcript in the document). Our recommendation is to perform differential expression it on normalized, rather than on raw data. 

Tools for differential expression are available on Gene/Transcript counts and on Normalized counts data nodes, under the RNA-Seq analysis section of the context sensitive menu. The possibilities are as follows:Partek Flow's powerful statistical analysis tools help identify differential expression patterns in the dataset. These can take into account a wide variety of data types and experimental designs.