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On the Affymetrix chip underlying the genome-wide expression studies, genes are often represented by multiple probe sets and thus, have multiple expression values.
In many instances, more than one probe-set matched to the same UniGene ID, resulting in multiple expression values for each such ID.
Therefore, a given gene can yield multiple expression values through microarray or next generation RNA sequencing (RNA-Seq) analyses.
However, to detect temporal patterns in gene expression, it is necessary to consider all time points, which requires simultaneous visualization of multiple expression values.
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Multiple expression value algorithms were used to control for variation among the algorithms and to generate a statistically stronger candidate gene set.
For genes represented by multiple probesets, expression values were averaged across probesets for randomization tests, heatmap visualization and GNS signature score calculation.
For genes with multiple probes, final expression values were the mean of the expression levels for multiple probes.
In addition, microarray data often brings in multiple missing gene expression values and noisy signals from the experiments.
For 277 transcripts targeted by multiple probes, mean expression values were calculated from the RMA expression data of all associated probes.
Significance thresholds and p-values are calculated for each transcript using multiple permutations of transcript expression values.
In gene set enrichment analysis using enrichment score [ 31], the expression value of the gene could be denoted by the mean of expression values of multiple probe sets that mapping to the same gene if these multiple probe sets are consolidated based on statistical tests.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com