Gene-expression profiling with reduced numbers of transcript measurements

A method of assaying gene expression, comprising:

• a) providing:
• i) a plurality of different barcode sequences;
• ii) a plurality of a solid support, each solid support comprising a homogeneous set of nucleic acid probes, each set complementary to a different barcode sequence of said plurality of barcode sequences;
• iii) a population of more than 1000 different transcripts, each transcript comprising a gene-specific sequence;
• iv) an algorithm capable of predicting the level of expression of unmeasured transcripts;
• b) processing said population of transcripts to create a plurality of different templates, each template comprising one of said plurality of barcode sequences operably associated with a different gene-specific sequence, wherein said plurality of different templates represents less than the total number of transcripts within said population;
• c) measuring the amount of each of said plurality of different templates to create a plurality of measurements;
• and
• d) applying said algorithm to said plurality of measurements, thereby predicting the level of expression of unmeasured transcripts within said population.