Adjust significance threshold (alpha) according to FDR (Benjamini & Hochberg)` method in R

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I'm aware about p.adjust function in R and it works well for my needs. However, now i'd like to correct significance threshold (alpha) instead of p-values themselves according to FDR (Benjamini & Hochberg) method.
For instance we have a ten of raw p-values:

0.0001,0.001,0.024,0.56,0.0077,0.55,0.0025,0.01,0.015,1

In case of Bonferroni it's very easy:

alpha_Bonferroni_corrected = 0.01/ number of tests (10 in our example)=0.001

But for FDR it will be a more tricky. Is there function in R for that?

asked Nov 10 at 22:17

Denis

7710

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up vote
3
down vote

favorite

0.0001,0.001,0.024,0.56,0.0077,0.55,0.0025,0.01,0.015,1

In case of Bonferroni it's very easy:

alpha_Bonferroni_corrected = 0.01/ number of tests (10 in our example)=0.001

But for FDR it will be a more tricky. Is there function in R for that?

asked Nov 10 at 22:17

Denis

7710

add a comment |

up vote
3
down vote

favorite

0.0001,0.001,0.024,0.56,0.0077,0.55,0.0025,0.01,0.015,1

In case of Bonferroni it's very easy:

alpha_Bonferroni_corrected = 0.01/ number of tests (10 in our example)=0.001

But for FDR it will be a more tricky. Is there function in R for that?

asked Nov 10 at 22:17

Denis

7710

0.0001,0.001,0.024,0.56,0.0077,0.55,0.0025,0.01,0.015,1

In case of Bonferroni it's very easy:

alpha_Bonferroni_corrected = 0.01/ number of tests (10 in our example)=0.001

But for FDR it will be a more tricky. Is there function in R for that?

asked Nov 10 at 22:17

Denis

7710

asked Nov 10 at 22:17

Denis

7710

asked Nov 10 at 22:17

Denis

7710

asked Nov 10 at 22:17

Denis

7710

asked Nov 10 at 22:17

Denis

7710

add a comment |

1 Answer
1

active

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votes

up vote
1
down vote

mutoss package seems to offer greater flexibility

 library(mutoss)

 alpha <- 0.01

 set.seed(1234)

 p <-c(runif(10, min=0, max=0.01), runif(10, min=0.9, max=1))

 result <- adaptiveBH(p, alpha)

 result

answered Nov 11 at 9:06

paoloeusebi

538312

Thanks for your reply. Unfortunately i was not able to install mutoss. Error: package or namespace load failed for ‘mutoss’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘multtest’. I tried: install.packages('multtest') and got: package ‘multtest’ is not available (for R version 3.4.0)
– Denis
Nov 11 at 10:59

1

Try this if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("multtest", version = "3.8"). bioconductor.org/packages/release/bioc/html/multtest.html
– paoloeusebi
Nov 11 at 11:38

Now i got it, thanks! But there is no ``FDR` corrected alpha in the result although. While it's probably to some extent easy to find the corrected alpha from the adaptiveBH R function output in comparison to p.adjust indeed. In the mentioned above your example adjusted alpha=(1/20)*0.01, but in case of multiple significant p-values it would not be clear.
– Denis
Nov 11 at 16:48

add a comment |

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1 Answer
1

active

oldest

votes

1 Answer
1

active

oldest

votes

up vote
1
down vote

mutoss package seems to offer greater flexibility

 library(mutoss)

 alpha <- 0.01

 set.seed(1234)

 p <-c(runif(10, min=0, max=0.01), runif(10, min=0.9, max=1))

 result <- adaptiveBH(p, alpha)

 result

answered Nov 11 at 9:06

paoloeusebi

538312

Thanks for your reply. Unfortunately i was not able to install mutoss. Error: package or namespace load failed for ‘mutoss’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘multtest’. I tried: install.packages('multtest') and got: package ‘multtest’ is not available (for R version 3.4.0)
– Denis
Nov 11 at 10:59

1

Try this if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("multtest", version = "3.8"). bioconductor.org/packages/release/bioc/html/multtest.html
– paoloeusebi
Nov 11 at 11:38

Now i got it, thanks! But there is no ``FDR` corrected alpha in the result although. While it's probably to some extent easy to find the corrected alpha from the adaptiveBH R function output in comparison to p.adjust indeed. In the mentioned above your example adjusted alpha=(1/20)*0.01, but in case of multiple significant p-values it would not be clear.
– Denis
Nov 11 at 16:48

add a comment |

up vote
1
down vote

mutoss package seems to offer greater flexibility

 library(mutoss)

 alpha <- 0.01

 set.seed(1234)

 p <-c(runif(10, min=0, max=0.01), runif(10, min=0.9, max=1))

 result <- adaptiveBH(p, alpha)

 result

answered Nov 11 at 9:06

paoloeusebi

538312

Thanks for your reply. Unfortunately i was not able to install mutoss. Error: package or namespace load failed for ‘mutoss’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘multtest’. I tried: install.packages('multtest') and got: package ‘multtest’ is not available (for R version 3.4.0)
– Denis
Nov 11 at 10:59

1

Try this if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("multtest", version = "3.8"). bioconductor.org/packages/release/bioc/html/multtest.html
– paoloeusebi
Nov 11 at 11:38

Now i got it, thanks! But there is no ``FDR` corrected alpha in the result although. While it's probably to some extent easy to find the corrected alpha from the adaptiveBH R function output in comparison to p.adjust indeed. In the mentioned above your example adjusted alpha=(1/20)*0.01, but in case of multiple significant p-values it would not be clear.
– Denis
Nov 11 at 16:48

add a comment |

up vote
1
down vote

mutoss package seems to offer greater flexibility

 library(mutoss)

 alpha <- 0.01

 set.seed(1234)

 p <-c(runif(10, min=0, max=0.01), runif(10, min=0.9, max=1))

 result <- adaptiveBH(p, alpha)

 result

answered Nov 11 at 9:06

paoloeusebi

538312

mutoss package seems to offer greater flexibility

 library(mutoss)

 alpha <- 0.01

 set.seed(1234)

 p <-c(runif(10, min=0, max=0.01), runif(10, min=0.9, max=1))

 result <- adaptiveBH(p, alpha)

 result

answered Nov 11 at 9:06

paoloeusebi

538312

answered Nov 11 at 9:06

paoloeusebi

538312

answered Nov 11 at 9:06

paoloeusebi

538312

answered Nov 11 at 9:06

paoloeusebi

538312

Thanks for your reply. Unfortunately i was not able to install mutoss. Error: package or namespace load failed for ‘mutoss’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘multtest’. I tried: install.packages('multtest') and got: package ‘multtest’ is not available (for R version 3.4.0)
– Denis
Nov 11 at 10:59

1

Try this if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("multtest", version = "3.8"). bioconductor.org/packages/release/bioc/html/multtest.html
– paoloeusebi
Nov 11 at 11:38

Now i got it, thanks! But there is no ``FDR` corrected alpha in the result although. While it's probably to some extent easy to find the corrected alpha from the adaptiveBH R function output in comparison to p.adjust indeed. In the mentioned above your example adjusted alpha=(1/20)*0.01, but in case of multiple significant p-values it would not be clear.
– Denis
Nov 11 at 16:48

add a comment |

Thanks for your reply. Unfortunately i was not able to install mutoss. Error: package or namespace load failed for ‘mutoss’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘multtest’. I tried: install.packages('multtest') and got: package ‘multtest’ is not available (for R version 3.4.0)
– Denis
Nov 11 at 10:59

1

Try this if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("multtest", version = "3.8"). bioconductor.org/packages/release/bioc/html/multtest.html
– paoloeusebi
Nov 11 at 11:38

Now i got it, thanks! But there is no ``FDR` corrected alpha in the result although. While it's probably to some extent easy to find the corrected alpha from the adaptiveBH R function output in comparison to p.adjust indeed. In the mentioned above your example adjusted alpha=(1/20)*0.01, but in case of multiple significant p-values it would not be clear.
– Denis
Nov 11 at 16:48

Thanks for your reply. Unfortunately i was not able to install mutoss. Error: package or namespace load failed for ‘mutoss’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘multtest’. I tried: install.packages('multtest') and got: package ‘multtest’ is not available (for R version 3.4.0)
– Denis
Nov 11 at 10:59

Try this if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("multtest", version = "3.8"). bioconductor.org/packages/release/bioc/html/multtest.html
– paoloeusebi
Nov 11 at 11:38

Now i got it, thanks! But there is no ``FDR` corrected alpha in the result although. While it's probably to some extent easy to find the corrected alpha from the adaptiveBH R function output in comparison to p.adjust indeed. In the mentioned above your example adjusted alpha=(1/20)*0.01, but in case of multiple significant p-values it would not be clear.
– Denis
Nov 11 at 16:48

add a comment |

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