Good microarray projects require many experiments and careful design of the study as indicated in the publication shown below

Microarray study design, example 1: comparison against different control samples (Ctl; control, e.g., a RNA derived from an unstimulated cell line; Ref; common reference, e.g. a pool of RNA derived from healthy donors)

Microarray study design, example 2: direct comparison of gene expression between two samples (a) or comparison of gene expression of the two samples (T, C) against a common reference (R) control sample.

Microarray study design, example 3: Dye-Swap experiments

Microarray study design, example 4: Variance and numbers of required experiments depending on the design of the study

Microarray study design, example 5: Potential design of time course experiments

Microarray study design, example 6: replicate experiments are mandatory to achieve significant results