Then we clustered probes with genomic distance <30 Kb, and we considered only probes belonging to at least a 2-probe cluster.
(B) Overview of hierarchically clustered probes.
However, bivalent H3K4/K27me3 marks much more often belonged to clustered probes compared to H3K4me3/DNAMe marks, which means that many of the H3K4/K27me3 sites colocalized in certain genes, and most of the H3K4me3/DNAMe sites were distributed separately with limited co-localization.
In k-means clustering, probes are clustered into k clusters for which the distances between probes within a cluster are small relative to the distance between clusters.
AffyProbeMiner has provided transcript consistent and gene consistent probe sets by clustering probes matching the same set of transcripts and genes [ 4].
The transcript level probe remapping used in this study is more appropriate as it clusters probes when they match the same set of transcripts [ 2- 4].
The major change from Dai's protocol was that probes were reorganized in transcript-level probe sets by clustering probes matching the same set of transcripts, in order to measure transcript level expression.
These values were hierarchically clustered by probe.
1 /*inter-cluster probe procedure*/.
Procedure 3: Inter-cluster probe procedure.
The inter-cluster probe procedure is a probe-based algorithm.
