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Pearson's correlation coefficients were computed to measure probe to probe expression patterns similarity for all possible gene pairs.
A total of 11 probes (starting with the sub-telomeric probe to probe RP11-387O17) were detected both on the full chromosome 17 and on Xqter of WI-38THP-1 cellsuggestinging a partial trisomy of these genomic areas, evidenced by probes on chromosome X.
The Derivative Log Ratio Spread (DRLS), a measure of probe to probe noise calculated by the CytoGenomics software, was used as a performance measure for hybridization quality.
The mean sample quality (QC) value as calculated by Nexus Copy Number™ software from Biodiscovery (measuring the probe to probe variance) was 0.19 (SD = 0.05).
Probe to probe variation is especially important when using arrays to look for copy number and/or presence or absence of genes in comparative studies.
Variations in intensity from probe to probe or chip to chip for samples need to be resolved to obtain a reliable level of expression.
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For both CQR and CQS gene expression data we computed the Spearman rank correlation, r, and a corresponding P-value using a t-statistic between each pfcrt probe to probes of each of the other genes.
Grouping such individual probes to probe sets resulted in 7,941 transcript-specific probe sets and 15,619 gene-specific probe sets.
We further mapped these probes to probe sets and there were 1,062 probe sets which include at least 3 probes belonging to the intersection.
In the effort of remapping the probes to probe sets for creating a custom Chip Definition File (CDF), Dai et al [ 15] defined one gene mapping one probe set to avoid "redundant probe sets" in gene chip analysis.
If the victim was wearing a beacon, use avalanche probes to probe the area where the signal is strongest.
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