In addition, the intensities detected by the microarrays for a gene will vary to some extent among the technical replicates due to the complex procedures of the microarray experiment, such as labeling, hybridization, and scanning.
RNA-seq has a wider dynamic range and avoids some of the technical limitations in a microarray experiment such as varying probe performance, cross-hybridization, limited dynamic range of individual probes, and nonspecific hybridization [ 4, 5].
In summary, incorporation of modified nucleotides may not only lead to discovery and better quantitation of rare expressers in complex samples but also impact other aspects of the microarray experiment such as probe design prior to array fabrication and the statistical design of microarray experiments.
Using quantitative multiplex PCR assay, the gene expression levels for several genes shown to be modulated according to the microarray experiments, such as apolipoprotein D (Apol D), E-cadherin, and cyclin A2, were confirmed.
This systematic variation might be due to technical differences between batches of microarray experiments, such as reverse transcription, labeling, hybridization, etc.
Standards for microarray experiments, such as MIAME [ 21], are evolving.
A table labelled "others" consists of information about non-transcriptomic DNA Microarray experiments such as genome comparisons.
These values were summed across all four microarray experiments such that extremes on either end of the distribution would be biased toward EST with large, significant differences.
This became possible with large public databases of microarray experiments such as the Gene Expression Omnibus (GEO) (Edgar et al., 2002) and ArrayExpress (Brazma et al., 2003).
Many potential sources of error can have a large impact on microarray experiments, such as inconsistency among multiple RNA extractions, reverse transcription, RNA amplification, and labeling, as well as different levels of background noise for each microarray.
It is conceivable that trimethylamine reduction increases the pH of the cytoplasm and, for this reason, other genes identified with microarray experiments, such as tryptophanase (PBPRB0382 and PBPRA2532) increase their expression in order to counter this alcalinization.
