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[[Image:Heatmap.png|right|thumb|Gene expression values from microarray experiments can be represented as [[heat map]]s to visualize the result of data analysis.]]
The advent of inexpensive microarray experiments created several specific bioinformatics challenges:<ref>{{Cite journal |last=Tinker |first=Anna V. |last2=Boussioutas |first2=Alex |last3=Bowtell |first3=David D.L. |date=2006 |title=The challenges of gene expression microarrays for the study of human cancer |url=https://doi.org/10.1016/j.ccr.2006.05.001 |journal=Cancer Cell |volume=9 |issue=5 |pages=333–339 |doi=10.1016/j.ccr.2006.05.001 |issn=1535-6108|doi-access=free }}</ref> the multiple levels of replication in experimental design ([[#Experimental design|Experimental design]]); the number of platforms and independent groups and data format ([[#Standardization|Standardization]]); the statistical treatment of the data ([[#Data analysis|Data analysis]]); mapping each probe to the [[mRNA]] transcript that it measures ([[#Annotation|Annotation]]); the sheer volume of data and the ability to share it ([[#Data warehousing|Data warehousing]]).
=== Experimental design ===
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