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An index of microarray platforms was compiled to aid in the comparison of microarray data.
A p-value significance cutoff of 0.05 (without any multiple testing correction) and a minimum absolute fold-change cutoff of 1.2 (typically the lowest sensitivity threshold of commercial microarray platforms) was used to obtain the final set of signatures of differentially-expressed genes.
Hybridization of total RNAs derived from SYT-SSX2 and pOZ vector-infectant transcripts to Affymetrix microarray platforms was performed and transcript changes were expressed as Log2 ratios of SYT-SSX2 signal intensity to pOZ control [where the Log2 ratio (x) represents 2x fold increases (or decreases) in transcript level].
In the present study, data from two different microarray platforms was used.
Profiling on the individual microarray platforms was done according to manufacturer's specifications.
Mapping across microarray platforms was done using the "Cleanex" database [ 14] to retrieve corresponding gene symbols and Affymetrix probe sets.
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Agilent 8x60K microarray platforms were used for these transcriptome analyses (Xuan et al. 2013).
Microarray platforms are capable of parallel genotyping of hundreds of thousands of SNPs in one measurement.
Third, two different microarray platforms were used in generating data for this study.
Because several different microarray platforms were used in those cohorts, we ensured that the probes were matched to identical genes.
Four microarray platforms were used in this analysis including; Agilent, Illumina, Affymetrix Exon 1.0 ST, and M430 arrays.
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