From - Genomics Technologies: The Power of Genome-Scale Quantitative Data Resolution Profiling Transcriptomes, Plant Physiology 2010
…More recently, direct sequencing of transcripts by high-throughput sequencing technologies (RNA-Seq) has become an additional alternative to microarrays and is superseding SAGE and MPSS (Busch and Lohmann, 2007). Like SAGE and MPPS, RNA-Seq does not depend on genome annotation for prior probe selection and avoids biases introduced during hybridization of microarrays. On the other hand, RNA-Seq poses novel algorithmic and logistic challenges, and current wet-lab RNA-Seq strategies require lengthy library preparation procedures. Therefore, RNA-Seq is the method of choice in projects using nonmodel organisms and for transcript discovery and genome annotation. Because of their robust sample processing and analysis pipelines, often microarrays are still a preferable choice for projects that involve large numbers of samples for profiling transcripts in model organisms with well-annotated genomes.
Table I. Advantages and disadvantages of various technologies for the measurement of transcript … abundance
Baginsky S, Hennig L, Zimmermann P, Gruissem W. (2010) Gene expression analysis, proteomics, and network discovery. Plant Physiol 152(2) 402-10. [article]