In contrast, Gardner's method requires both measurements of mRNA concentrations and measurements of the applied rate perturbations, which is not usually part of a standard microarray experimental protocol.
The RNA processing and microarrays experimental protocols were performed in the University of Pennsylvania Microarray Core Facility.
These values are much lower than those observed in comparisons between EW and LW [ 45], and between juvenile and mature wood [ 46] using the same cDNA microarrays and experimental protocols.
The Minimum Information About a Microarray Experiment (MIAME) (Brazma, 2009) initiative targets experimental protocols in microarray experiments and other 'omics' studies, while the REMARK guidelines (Altman et al., 2012) focus on the appropriate and transparent use of statistical methods in tumour marker prognostic studies.
The microarray raw data and experimental protocols were deposited in the Arrayexpress database (accession No. E-MTAB-3313 E-MTAB-3313 E-MTAB-3313
Due to the different microarray platforms (Affymetrix, Agilent Technologies), experimental protocols and data processing for normalization used by authors, we choose to use gene expression raw data individually.
However, it is worthwhile noting that integrating microarray datasets from different studies is not so simple due to the different microarray platforms across different datasets, different experimental protocols, and different preprocessing methods.
The experimental protocols and raw microarray data can be found in ArrayExpress under the accession number E-MEXP-1261 E-MEXP-1261 E-MEXP-1261
The experimental protocols and the raw microarray data can be found in ArrayExpress under the accession number E-MEXP-2502 E-MEXP-2502 E-MEXP-2502
Critical to its success is the establishment of a microarray database with high storage and computational capacity, development of standardized experimental protocols, novel analytical approaches, customized analytical tools, and design oligonucleotides for microarray expansion.
