Table 1.

Comparison of cDNA and oligonucleotide microarrays

Feature	Oligonucleotide microarrays	Spotted microarrays
Typical probe length	18 – 30 mers	500 – 1000 base pairs (cDNA) 25 – 100 mers (oligo)
Spot density	> 500,000 features per slide	≤ 80,000 spots per slide
Hybridization Specificity	High specificity	Not as specific with possible cross-hybridization
Expression levels	Normalized for single-channel system	Ratio-based normalization for dual-channel system
Advantages	• Large-scale production • Highly reproducible • Detection of alternative splice variants • Precise measurements • Information can still be generated for genes without expression in the reference/control sample	• Lower costs • Signal amplification is not needed • Independent of genome sequence • Elimination of artifacts from spotting
Disadvantages	• Expensive • Few producers of necessary equipment and buffers • Difficulty detecting low abundance transcripts	• Hybridization is dependent upon length of sequences spotted • Labeling efficiency of dyes is an issue • Little information is generated for genes without expression in the reference/control sample • Handling of clones