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Cluster dendrogram drawn by pvclust methods using R software exhibited gene expression pattern was not remarkably affected during chemotherapy.
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Cluster analysis was performed using pvclust v.1.3.2 using the ward.D2 method with 10,000 bootstraps [ 39].
The correct classification of the samples as either infected treatments (clustering together) or uninfected controls (as outgroups) was confirmed with hierarchical clustering implemented in the R package "pvclust" [ 102], using complete Euclidean distance with 1000 bootstrap replicates.
To classify SCLC from other lung cancer types, unsupervised clustering of the SSHN genes was performed by bootstrapping analysis using pvclust package [ 69].
For bootstrap sampling confidence measures to determine the stability of the clustering, we used pvclust which uses hclust internally.
To evaluate confidence in the clustering results, the R bootstrap resampling package pvclust was used.
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