calcPosteriorProbNull: Title Calculate FDR adjusted threshold for posterior...

In satabdisaha1288/scBT: What the Package Does (One Line, Title Case)

Title Calculate FDR adjusted threshold for posterior probabilities of the null distribution Newton, Michael A., Amine Noueiry, Deepayan Sarkar, and Paul Ahlquist. "Detecting differential gene expression with a semiparametric hierarchical mixture method." Biostatistics 5, no. 2 (2004): 155-176. Tadesse, Mahlet G., Joseph G. Ibrahim, Robert Gentleman, Sabina Chiaretti, Jerome Ritz, and Robin Foa. "Bayesian Error‐in‐Variable Survival Model for the Analysis of GeneChip Arrays." Biometrics 61, no. 2 (2005): 488-497.

Description

Title Calculate FDR adjusted threshold for posterior probabilities of the null distribution Newton, Michael A., Amine Noueiry, Deepayan Sarkar, and Paul Ahlquist. "Detecting differential gene expression with a semiparametric hierarchical mixture method." Biostatistics 5, no. 2 (2004): 155-176. Tadesse, Mahlet G., Joseph G. Ibrahim, Robert Gentleman, Sabina Chiaretti, Jerome Ritz, and Robin Foa. "Bayesian Error‐in‐Variable Survival Model for the Analysis of GeneChip Arrays." Biometrics 61, no. 2 (2005): 488-497.

Title Calculate FDR adjusted threshold for posterior probabilities of the null distribution Newton, Michael A., Amine Noueiry, Deepayan Sarkar, and Paul Ahlquist. "Detecting differential gene expression with a semiparametric hierarchical mixture method." Biostatistics 5, no. 2 (2004): 155-176. Tadesse, Mahlet G., Joseph G. Ibrahim, Robert Gentleman, Sabina Chiaretti, Jerome Ritz, and Robin Foa. "Bayesian Error‐in‐Variable Survival Model for the Analysis of GeneChip Arrays." Biometrics 61, no. 2 (2005): 488-497.

Usage

calcPosteriorProbNull(
  bayes.out,
  kappa = seq(0.01, 1, 0.01),
  alpha = c(0.01, 0.05)
)

calcPosteriorProbNull(
  bayes.out,
  kappa = seq(0.01, 1, 0.01),
  alpha = c(0.01, 0.05)
)

Arguments

kappa	: sequence of thresholding values preferably; kappa<-seq(0.01,1,0.01)
alpha	: Desired FDR (False Discovery Rate) level
DETest_output_Bayes	: named (gene-names) vector of Bayes Factor values obtained from the Bayes Test

Value

max_kappa : Threshold value: Reject all hypothesis with posterior null probabilies less than max_kappa

max_kappa : Threshold value: Reject all hypothesis with posterior null probabilies less than max_kappa

Author(s)

Satabdi Saha

Satabdi Saha

satabdisaha1288/scBT documentation built on June 1, 2025, 4:06 p.m.