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Selected the most variable CpGs per gene for clustering in both datasets.

Batch removed:

[[1]]
[1] "cg11262815" "cg11248413" "cg14182690" "cg06295404" "cg10990993"
[[2]]
[1] "CACNA1G" "NEUROG1" "RUNX3"   "SOCS1"   "MLH1"

Batch, age and gender removed:

[[1]]
[1] "cg11262815" "cg11248413" "cg14182690" "cg06295404" "cg10990993"
[[2]]
[1] "CACNA1G" "NEUROG1" "RUNX3"   "SOCS1"   "MLH1"

Heatmaps (left - batch removed, right - batch, age, gender)

Methylation > Laird markers on 27k platform > Colon_Tumor_BatchRemoved_LairdGenesHeatmap.png

pvclust didn't work on these datasets:

Error in solve.default(crossprod(X, X/vv)) : 
  Lapack routine dgesv: system is exactly singular
In addition: Warning message:
In lsfit(X, zz, 1/vv, intercept = FALSE) : 'X' matrix was collinear