Question

1) Microarrays are notoriously difficult to reproduce. (i.e. You rarely get the same results twice). Explain why this might be.

2) Since microarrays are so difficult to reproduce, validation of the microarray results is crucial. What would be a great method to verify your microarray results?

Answer 1

1) One of the reasons for difficulty in reproducibility of microarray data could be the application of Pearson's correlation. In this, value to one indicates a good reproducibility. But Pearson's correlation assumes that the variance along the data is equal when the variance along the spots in microarray varies. Another is the presence of cross-hybridization signals in the probes for cDNA and oligonucleotide microarrays, which might prevent the detection of large changes in the gene expression levels.

2) The best way to validate microarray data is by RT-qPCR. Though Northern Blot is the best option for transcriptional assays, time and the quantity of RNA needed is high. Hence, RT-qPCR is preferred.