How does MPSS compare to microarrays?
MPSS offers several advantages over microarrays, although cost and turn-around time are certainly not included in those advantages. Microarray expression analysis is subject to inherent limitations that include: sensitivity to the quantity of RNA hybridized to the chip; background intensities rivaling signals for weakly expressed transcripts; and difficulty distinguishing between closely related sequences. MPSS is less sensitive to RNA quantities, because as many molecules are sequenced as needed. Background is significantly lower in MPSS, because it results only from errors in sequencing; we use a cutoff of ~3 TPM as the background. MPSS can often but not always distinguish closely related sequences; because it depends on sequencing, it is only necessary that the gene have a UNIQUE 17 bp signature in the proper location relative to it’s most close relatives. Microarrays require standardization and calibration to ensure proper comparisons of hybridization patterns are made across diver
