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In cases with multiple probes per gene the most variable probe was selected, resulting in 18,295 unique genes.
In cases with multiple probes per gene the most variable probe was selected, resulting in 18,295 unique coding genes.
An InterQuartile Range was calculated across all samples for each probe, and used to select the most variable probe of those that mapped to the same transcript.
We then selected the most variable probe sets per gene (n=17 583), and of these, the 5000 most variable probe sets on FFPE expression profiles.
The overlap between the most variable probe sets in FF tissue and the most variable probe sets in FFPE tissue (FF: 5000/FFPE: 17 853) consisted of 4620 matching probe sets.
Similar to [ 4, 60] we chose the most variable probe set for each gene as a representative in this article.
Similar(46)
For clustering analysis of 122 samples, the standard deviation of β-values for each probe was calculated, and the top 10,000 most variable probes were selected.
We found no significant enrichment for this subset of probes in any set of our GR or ER hits, when using either the entire genome or the subset of ∼2,000 most variable probes as the background set.
The most variable probe-sets were used to cluster 120 familial samples using average linkage hierarchical clustering with correlation as a distance metric.
Unsupervised clustering on approximately 3,500 of the most variable probes resulted in two distinct clusters.
The microarray dataset was filtered before clustering in order to select the 2,000 most variable probes.
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