A linear regression was applied to the cluster of ratios generated from the standard reference DNA samples and used to calibrate the inference of copy number from the ratios of the unknown samples.
To characterize these commonly up-regulated genes in more detail, first we performed hierarchical cluster analysis (based on average linkage clustering of ratios) comparing human 2fTGH with hST2-U3C and mouse MEF-WT with mST2-MS1KO.
This cluster of ratio values is called a ratio-cluster (RC).
We created a program, denoted ClusterA, for calculating numeric "Silhouettes" for clustered data, such as for example the three clusters of signal ratios commonly obtained in SNP genotyping assays.
Closer investigation of the distribution of aCGH log2 intensity ratio scores at this locus (Figure S6) identified a cluster of log2 ratios at −5.0, 0.0 and 1.0, which would appear to be consistent with a heterozygous deleted reference sample, so that the cluster at 1.0 corresponds to undeleted samples with a copy number of two.
One way Hierarchical clustering of the ratios (Control vs. Stress) of significantly differentially expressed genes were performed in JMP Genomics using the default settings of ten clusters.
Moreover, a sliding window analysis of the distribution of the M F ratio of genes on the Z chromosome did not reveal any apparent clusters of similar M F ratios consistent across tissues.
At the second layer, nodes are organized in clusters of k-hop ratio (i.e., by nodes up to k-hops away the central node, the cluster head).
Since the number of births often remains limited when disaggregated for the 70-odd administrative provinces of Viet Nam, we have used a geostatistical technique to identify the clusters of high sex ratio in the country [26].
Hierarchical clustering of z-ratio data using Genesis software [21] was used to assess the overall relatedness of the global transcriptional changes for all drug abuse cases.
Hierarchical clustering of log2 ratio scale copy number values was performed with the Euclidean distance metric and complete linkage clustering.
