Variant genotyping methods were used, which included polymerase chain reaction restriction fragment length polymorphism assay (PCR-RFLP) in 14 studies, TaqMan assay, MassARRAY, microarray, arrayed primer extension (APEX) and unknown method in one study each.
An advantage of our system over other tag-array methods is the software developed for analysis of the microarray data.
All microarrays were normalized by TAIR using the robust multi-array method (RMA).
A membrane-array method was developed for the detection of human intestinal bacteria in fecal samples without using the expensive microarray-arrayer and laser-scanner.
However, throughput is greatly reduced, relative to endpoint analysis of agar spotted arrays, or the use of DNA microarray hybridization methods [ 4, 8, 17- 19].
Although Infinium HumanMethylation450 is a two-color channel microarray, the methods developed previously for gene expression arrays cannot be used as such.
In comparing Affymetrix microarray normalization methods, Bolstad et al [11] perform variance, pairwise and bias comparisons between arrays.
Most microarray normalization methods assume that the total mRNA quantity will remain constant across the different arrays and time points.
Given the lack of consensus within the bioinformatics community regarding the different microarray normalization methods [15], we analyzed our data using two different algorithms: GC-Robust Multi-Array (GCRMA) [16] and dChip [17].
In other words, it appears that a better correlation was observed between SAGE and oligonucleotide arrays, than between both DNA microarray methods.
