UNM Health Sciences Center: Keck-UNM Genomics Resource

Affymetrix microarrays cost more than glass slide arrays, but perform 12 separate measurements on each gene. Having so many measurements allows the software to perform statistical (t-test) analyses on whether each gene is expressed at a statistically significant level above the background.

To get statistically significant data with glass slide (spotted) arrays that have only one spot per gene requires at least three arrays per RNA sample.

Affymetrix GeneChips provide higher quality data, include more controls and require much less RNA than a similar analysis using glass slide arrays.

Affymetrix GeneChips are available for human, mouse, rat, yeast and other genomes.

	Glass Slide Arrays	Affymetrix GeneChips
Typical cost per array	$ 80.00	$ 450.00
Arrays needed per 40,000 genes	2	1
Measurements per gene on each array	1	12
Arrays needed to achieve at least three measurements per gene	6	1
Array cost per sample	$ 480.00	$ 450.00
Typical amount of total RNA needed per array	10 µg	0.1 – 1 µg
Total amount of RNA needed from each sample	> 30 µg	< 1 µg
Total arrays needed for a three-condition experiment (e.g. untreated, vehicle, drug), performed in duplicate	36	6
Total array cost (6 samples)	$ 2,880.00	$ 2,700.00


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