LumiWCluster

[…] with missing values, those residing on the x chromosome, and those with a median detection p-value >0.05 across samples can be filtered out; other packages allowing such filtering include (; )., lumiwcluster () includes a function for model-based clustering of methylation data using a weighted likelihood approach wherein higher-quality samples (i.e., those with a low median detection […]

[…] in hpv(+) and hpv(−) tumors. the effects of clinical characteristics on dna cpg methylation measured on the goldengate array were examined using limma in r 2.10.1 . sample weights generated with lumiwcluster based on detection p-values across samples were used in the lmfit function from the limma package to downweight samples with higher detection p-values. cpg sites were identified […]

[…] island methylator phenotype (cimp) were validated using rand index., methylation data from tumour samples were normalised for sequence length and gc content, and important probes were selected using lumiwcluster package, thus eliminating arbitrary detection p-value cutoffs in removing unreliable methylation values (). wilcoxon rank sum test was employed in identifying statistically significant […]