Abstract: The present invention relates to methods and probes for detecting relative levels of multiple nucleic acid sequences of interest. The invention includes a method to detect the relative amounts of at least two target nucleic acid sequences in at least one sample by use of a corresponding set of detectably labelled oligonucleotide probes for each of the at least two target nucleic acid sequences, and detecting the hybridization of each of the corresponding sets of oligonucleotide probes to its respective target nucleic acid sequence. The invention also includes a method to detect the relative amounts of multiple target messenger RNAs in at least one microscopy sample by in situ hybridization using sets of oligonucleotide probes. Also disclosed are methods to provide corresponding sets of oligonucleotide probes for target nucleic acid sequences.