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

up vote
3
down vote

favorite

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

7210

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

7210

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

7210

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

7210

asked Nov 10 at 22:17

Denis

7210

asked Nov 10 at 22:17

Denis

7210

asked Nov 10 at 22:17

Denis

7210

asked Nov 10 at 22:17

Denis

7210

add a comment |

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

528211

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 |

Your Answer

StackExchange.ifUsing("editor", function () {
StackExchange.using("externalEditor", function () {
StackExchange.using("snippets", function () {
StackExchange.snippets.init();
});
});
}, "code-snippets");

StackExchange.ready(function() {
var channelOptions = {
tags: "".split(" "),
id: "1"
};
initTagRenderer("".split(" "), "".split(" "), channelOptions);

StackExchange.using("externalEditor", function() {
// Have to fire editor after snippets, if snippets enabled
if (StackExchange.settings.snippets.snippetsEnabled) {
StackExchange.using("snippets", function() {
createEditor();
});
}
else {
createEditor();
}
});

function createEditor() {
StackExchange.prepareEditor({
heartbeatType: 'answer',
convertImagesToLinks: true,
noModals: true,
showLowRepImageUploadWarning: true,
reputationToPostImages: 10,
bindNavPrevention: true,
postfix: "",
imageUploader: {
brandingHtml: "Powered by u003ca class="icon-imgur-white" href="https://imgur.com/"u003eu003c/au003e",
contentPolicyHtml: "User contributions licensed under u003ca href="https://creativecommons.org/licenses/by-sa/3.0/"u003ecc by-sa 3.0 with attribution requiredu003c/au003e u003ca href="https://stackoverflow.com/legal/content-policy"u003e(content policy)u003c/au003e",
allowUrls: true
},
onDemand: true,
discardSelector: ".discard-answer"
,immediatelyShowMarkdownHelp:true
});

}
});

draft saved

draft discarded

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

StackExchange.ready(
function () {
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fstackoverflow.com%2fquestions%2f53243979%2fadjust-significance-threshold-alpha-according-to-fdr-benjamini-hochberg-m%23new-answer', 'question_page');
}
);

Post as a guest

Name

Required, but never shown

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

528211

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

528211

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

528211

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

528211

answered Nov 11 at 9:06

paoloeusebi

528211

answered Nov 11 at 9:06

paoloeusebi

528211

answered Nov 11 at 9:06

paoloeusebi

528211

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 |

draft saved

draft discarded

draft saved

draft discarded

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

Post as a guest

Name

Required, but never shown

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

Sign up or log in

StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});

Post as a guest

Name

Required, but never shown

Name

Required, but never shown

Name

Required, but never shown

This page is only for reference, If you need detailed information, please check here

搜尋此網誌

Nrthugu