Wednesday, November 25, 2009

Microarray versus Sequencing

See the paper here:

Conclusion: Our analysis of next generation sequencing was motivatedby the rapidly converging cost of microarray analysis witha single lane of data from the next generation sequencer. In summary, our results indicate that, at least for the present, microarrays remain a highly competitive technology forquantitative measurement of differential gene expression. Arrays have an advantage in measuring low-abundance transcripts. Also, the current throughput of array experiments is higher than the 8 lanes present on an the NGS instrument. It is routine to process 24–96 arrays in asingle day, while the NGS instrument is limited to 8 lanes that require approximately 48 hours to run. Multiplexing approaches can increase the number of samples per lane of the instrument, but our analysis suggests thataccurate analysis of gene expression in yeast by full-length cDNA sequencing requires at least the entire output of a single lane. More lanes may be necessary in other species with more complex mRNA pools.