Since microarray measures are inherently corrupted by noise, we hypothesized that the true underlying biological correlations between gene expression and H3K9 acetylation were much greater than captured through a simple correlation of high SNR genes.
Overall correlation between the microarray and frequency-based expression measures was modest.
The 3′/5′ intensity gradient, the basis of microarray RNA quality measures, is shown to depend on the degree of competitive binding of specific and of non-specific targets to a particular probe, on the degree of saturation of the probes with bound transcripts and on the distance of the probe from the 3′-end of the transcript.
A precisely linear relationship between the microarray and qPCR measurements is not necessarily expected because the microarray features are capable of measuring methylation of a larger local region (1 to 4 Kb) than the qPCR amplicons were designed to interrogate (400 600 bp).
Second, to answer the call for transparency in data documentation [17], [18], we developed a scoring system based on our understanding of what the system was designed to reveal and what the cellular microarray system was measuring.
Relative expression of the miRNAs identified from microarray analysis was measured by real-time PCR.
The first Saccharomyces cerevisiae cell cycle microarray dataset was measured through the regulatory responses under the elutriation treatment, available at the Stanford Microarray Database.
Since the microarray data was measured by the ratio of the hybridization signal for each gene, it could vary by factors of 2 or greater.
The quality of RNA used for microarray analysis was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), according to the manufacturer's instructions.
For example, a decreased expression of Trp53 in microarray analysis was measured only in two probe sets that recognise multiple alternative transcripts from the same gene each, whereas a third definite probe set did not recognise any modulation of expression.
