Application of a correlation correction factor in a microarray cross-platform reproducibility study.

BACKGROUND: Recent research examining cross-platform correlation of gene expression intensities has yielded mixed results. In this study, we demonstrate use of a correction factor for estimating cross-platform correlations. RESULTS: In this paper, three technical replicate microarrays were hybridized to each of three platforms. The three platforms were then analyzed to assess both intra- and cross-platform reproducibility. We present various methods for examining intra-platform reproducibility. We also examine cross-platform reproducibility using Pearson's correlation. Additionally, we previously developed a correction factor for Pearson's correlation which is applicable when X and Y are measured with error. Herein we demonstrate that correcting for measurement error by estimating the "disattenuated" correlation substantially improves cross-platform correlations. CONCLUSION: When estimating cross-platform correlation, it is essential to thoroughly evaluate intra-platform reproducibility as a first step. In addition, since measurement error is present in microarray gene expression data, methods to correct for attenuation are useful in decreasing the bias in cross-platform correlation estimates.

Supramolecular nanostamping: using DNA as movable type.

Here we present a novel printing technique (that we call supramolecular nanostamping), based on the replication of single-stranded DNA features through a hybridization-contact-dehybridization cycle. On a surface containing features each made of single-stranded DNA molecules of known sequence, the complementary DNA molecules are hybridized, spontaneously assembling onto the original pattern due to sequence-specific interactions. These complementary DNA strands, on the end that is assembled far from the original surface, are 5' modified with chemical groups ("sticky ends") that can form bonds with a target surface that is brought into contact. Heating induces dehybridization between DNA strands, leaving the original pattern on the original surface and the copied pattern on the secondary substrate, and thus stamping (see Figure 1). Molecular recognition provides the unique and disruptive ability of transferring large amounts of information in a single printing cycle, that is the simultaneous stamping of spatial information (i.e., the patterns) and of chemical information (i.e., the features' DNA sequence--their chemical composition). This method combines high resolution (<40 nm) with the advantage of an exponential increase in the number of masters; in fact, any printed substrate can be reused as a master. Patterns fabricated via very different lithographic techniques can be replicated.