Cytokines, chemokines and adhesion molecules were analysed on the Evidence® array biochip analyser (Randox Laboratories Ltd., Crumlin, UK) [ 25].
Scanned microarrays were analysed using Array-Pro Analyser (MediaCybernetics, USA) and presented as heat maps in which colour intensity was correlated to mean spot signals.
Fluorescent images were scanned using a Tecan LS Reloaded Scanner (Tecan Trading AG) and the analysis software Array-Pro Analyser (Media Cybernetics, Inc., Bethesda, MD, USA).
Three software packages that are commonly used for processing copy number data on Affymetrix SNP arrays are Copy Number Analyser for GeneChip arrays (CNAG) [CNAG, 56], DNA-Chip Analyzer (dChip) [dChip, 47] and Affymetrix GeneChip Chromosome Copy Number Analysis Tool (CNAT CNATAT, [ 57]).
Lactate dehydrogenase was tested on a Beckman LX20 instrument (Beckman Instruments, Gagny, France), and CRP was assayed by a rate immunonephelometric technique on a protein system analyser (BN2 Array; Dode-Behring, Munich, Germany).
This output is then used by a Hidden Markov Model (HMM) to infer CNs [ 44]. Copy Number Analyser for GeneChip arrays (CNAG) [ 45] normalizes the arrays in order to have the same mean signal intensity for all autosomal probes.
This output is then used by a Hidden Markov Model (HMM) to infer CNs [ 44 ]. iii) Copy Number Analyser for GeneChip arrays (CNAG) [ 45 ] normalizes the arrays in order to have the same mean signal intensity for all autosomal probes.
Levels of IL-10 and IFN-γ were quantified by a cytokine biochip array on the Evidence Investigator analyser following the manufacturer's instructions (Randox Laboratories Ltd., Crumlin, UK).
Serum samples were collected and used for simultaneous determination of IL-10 and sCD25, using a cytokine biochip array on the Evidence Investigator analyser (Randox Laboratories Ltd ,Crumlin, UK), while PCT was assayed by an enzyme-linked fluorescent assay (VIDAS BRAHMS PCT; bioMerieux, France).
With the array of sampling techniques and analysers available, standardised protocols and cut off data should be developed.
Baross et al found considerable variation among the outputs from different programs, as well as substantial false call rates for CNVs, when they compared four CNV detection programs [20]: Copy Number Analyser for GeneChip® arrays (CNAG) [21], DNA-Chip Analyzer (dChip) [22], Affymetrix GeneChip® Chromosome Copy Number Analysis Tool (CNAT [20], [23] and Gain or Loss Analysis of DNA (GLAD) [24].
