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Multiple probes from the same HUGO gene ID were averaged, and HUGO gene IDs with less than 70% valid data were removed, leaving ∼24K genes.
In studies containing multiple probes from a given gene symbol, one was randomly selected and subject to analyses.
A particular goal is to generate multiple probes from alternative scaffolds to unveil potential off-target effects.
The median of signals from multiple probes (from coding and non-coding strand) for each individual gene was calculated using R, from which log2 expression values were derived.
When multiple probes from one platform were mapped to one probe from the other platform, a one to one probe pair was randomly selected.
Multiple probes from the same gene were converted to a mean, patients were grouped based on expression levels and Kaplan Meier survival was plotted.
Similar(51)
Hybridization signals from multiple probes for each target strain were integrated using a novel algorithm for data analysis.
A gene was said to be detected at p < 0.05 level if the mean signal intensity from multiple probes for that gene was significantly higher (at the level of p < 0.05) than the negative control on the same chip.
A locus was said to be detected at p < 0.05 level if the mean signal intensity from multiple probes for that CpG locus was significantly higher (at the level of p < 0.05) than the negative control on the same chip.
We select a single probe for each gene to further avoid biases in gene set tests from using multiple probes for a single gene.
To avoid potential technical variations between probes, the methylation levels of multiple probes for a single gene (average of four probes per gene) were not collapsed or averaged, and genes having multiple discordant probe intensities were eliminated from the analysis.
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