This functions returns the adjusted significance level from the screening stage that should be used to compare confirmation stage FWER adjusted p-values against.
1 2 3 4 5 6 7
an object of the
The adjusted significance level is calculated as the fraction of significant features in the screening stage multiplied the alpha level.
Scalar, the adjusted significance level from the screening stage.
stageRTx: Get adjusted significance level from the screening stage.
Van den Berge K., Soneson C., Robinson M.D., Clement L. (2017). stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biology 18:151. https://doi.org/10.1186/s13059-017-1277-0
R. Heller, E. Manduchi, G. R. Grant, and W. J. Ewens, "A flexible two-stage procedure for identifying gene sets that are differentially expressed." Bioinformatics (Oxford, England), vol. 25, pp. 1019-25, 2009.
1 2 3 4 5 6 7 8
pScreen=c(seq(1e-10,1e-2,length.out=100),seq(1e-2,.2,length.out=100),seq(.2,1,length.out=100)) names(pScreen)=paste0("gene",1:300) pConfirmation=matrix(runif(900),nrow=300,ncol=3) dimnames(pConfirmation)=list(paste0("gene",1:300),c("H1","H2","H3")) stageRObj <- stageR(pScreen=pScreen, pConfirmation=pConfirmation, pScreenAdjusted=FALSE) stageRObj <- stageWiseAdjustment(stageRObj, method="holm", alpha=0.05) adjustedAlphaLevel(stageRObj) # @method stageR-method
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.