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Table 1 Comparison of cDNA and oligonucleotide microarrays

From: A perspective on microarrays: current applications, pitfalls, and potential uses

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