The best replacement for microarray is rna seq.

The best alternatives to microarray are rated as following:
★★★★★  rna seq
★★★★★  pcr
★★★★  qpcr
★★★  fish
★★★  karyotype
★★★  sequencing
★★★  northern blot
★★★  real time pcr
★★  ngs
★★  sage
★★  microarray
★★  rna sequencing
★  deep sequencing
★  rt-pcr
★  cgh
★  rt pcr
★  next gen sequencing
★  southern blot
★  rna-seq
★  exome sequencing
★  next generation sequencing
★  northern blotting
★  traditional amniocentesis
  affymetrix
  qrt pcr
  oligonucleotide microarray

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