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Question: Insignificant q-values in minfi
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4.4 years ago by
Guest User12k
Guest User12k wrote:
Hello List, I am analyzing 450 k methylatio data using minfi package and getting large (~1) q-values. I want to remove the probes with lower variance to improve q-value (so that there will be less test(multiple test corection ). How can I do this in beta values object prior to using dmpfinder function? Thanks for help. code used: gRatioSet.quantile <- preprocessQuantile(RGset, fixOutliers = TRUE, removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize = TRUE, stratified = TRUE, mergeManifest = FALSE, sex = NULL) colnames(gRatioSet.quantile) beta<-getBeta(gRatioSet.quantile) nrow(beta) Beta.noSNPs=rmSNPandCH(beta, dist = 2, mafcut = 0.05) ### removing SNP probes nrow(Beta.noSNPs) dmp <- dmpFinder(Beta.noSNPs, pheno=pData(gRatioSet.quantile)$Sample_Group, type="categorical") ### methylated sites head(dmp,n=100) -- output of sessionInfo(): > head(dmp,n=100) intercept f pval qval cg19314777 0.85646150 23.31203 3.057187e-05 0.9417651 cg15306012 0.60817234 23.23892 3.125969e-05 0.9417651 cg01224520 0.81419046 23.19462 3.168447e-05 0.9417651 cg08515264 0.81986249 23.18189 3.180761e-05 0.9417651 cg25110423 0.79139248 22.89596 3.471317e-05 0.9417651 cg11642412 0.19004546 22.71170 3.673422e-05 0.9417651 cg26331096 0.70306567 22.46844 3.959597e-05 0.9417651 -- Sent via the guest posting facility at bioconductor.org.
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