Selection of normalization methods based on golden standards (FDR and FNR)
fig.FDR_FNR.RdFunction for boxplot of FDR and FNR based on the DEA from the golden benchmark (typically
the data set data.benchmark) and the normalized test dataset (typically the
normalized or raw data set data.test)
fig.FDR_FNR(DEA, truth.DEA, title, subset = NULL)Arguments
| DEA | a list of differential expression analysis results with the element names to be the normalization methods |
|---|---|
| truth.DEA | differential expression analysis results from the benchmark (gold standard) obtained from DE.voom, DE.edge, or any method from the users by storing the results as same as DE methods in the package (including DE genes, p-values and log2 fold changes) |
| title | Figure title |
| subset | optional Vector of a subset of markers.
If given, the plot will be limited to the given subset
of markers. Leave |
Value
figure for selection of normalization methods
Examples
voom.benchmark <- DE.voom(data.benchmark, data.group)
test.norm <- pip.norm(raw=data.test, groups=data.group, norm.method = "all")
#> converting counts to integer mode
test.DE <- list(
TMM = DE.voom(RC=test.norm$TMM$dat.normed, groups = data.group),
TC = DE.voom(RC=test.norm$TC$dat.normed, groups = data.group),
UQ = DE.voom(RC=test.norm$UQ$dat.normed, groups = data.group),
med = DE.voom(RC=test.norm$med$dat.normed, groups = data.group),
DESeq = DE.voom(RC=test.norm$DESeq$dat.normed, groups = data.group),
PoissonSeq = DE.voom(RC=test.norm$PoissonSeq$dat.normed, groups = data.group),
QN = DE.voom(RC=test.norm$QN$dat.normed, groups = data.group),
RUVg = DE.voom(RC=data.test, groups = data.group, normalized=FALSE, adjust=test.norm$RUVg$adjust.factor),
RUVs = DE.voom(RC=data.test, groups = data.group, normalized=FALSE, adjust=test.norm$RUVs$adjust.factor),
RUVr = DE.voom(RC=data.test, groups = data.group, normalized=FALSE, adjust=test.norm$RUVr$adjust.factor),
SVA = DE.voom(RC=data.test, groups = data.group, normalized=FALSE, adjust=test.norm$SVA$adjust.factor),
noNorm = DE.voom(RC=data.test, groups = data.group))
fig.FDR_FNR(DEA = test.DE, truth.DEA = voom.benchmark, title = "Example of FDR FNR scatterplot")
