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Posts by belinda.phipson
... Hi Evani I'm not 100% sure I understand your question. The plotBias=TRUE produces a plot that shows the proportion of signficantly differentially methylated (DM) genes in bins of ~ 200 genes. The bins are allocated based on the numbers of CpGs annotated to each gene. So each point in the plot repre ...
... Hi Philipp, I just wanted to add a comment about the warning message. In the mapping of CpGs to gene symbols and subsequently to Entrez GeneIDs, I use the alias2SymbolTable to get the most up to date symbols to map to Entrez GeneID. This function always spits out this warning message, and I don't b ...
... Hi Ed, Do you mean that you want to use the output from the pwf function to adjust the p-values obtained from a differential methylation analysis? This is circular logic in that you need to first perform the differential methylation analysis, impose some sort of cut-off criteria to specify which pr ...
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