R Observatory: Metrics for fmt version 2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

fmt

2.0

Variance Estimation of FMT Method (Fully Moderated T-Statistic)

0packages depend

2.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Lianbo YuFirst published 2012-08-302 releasesCRAN page ↗

The FMT method computes posterior residual variances to be used in the denominator of a moderated t-statistic from a linear model analysis of gene expression data. It is an extension of the moderated t-statistic originally proposed by Smyth (2004) doi:10.2202/1544-6115.1027. LOESS local regression and empirical Bayesian method are used to estimate gene specific prior degrees of freedom and prior variance based on average gene intensity levels. The posterior residual variance in the denominator is a weighted average of prior and residual variance and the weights are prior degrees of freedom and residual variance degrees of freedom. The degrees of freedom of the moderated t-statistic is simply the sum of prior and residual variance degrees of freedom.

Install

R (CRAN)Ubuntu (r2u)

install.packages("fmt", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-fmt

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 54 s · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

1

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.6K

CRAN downloads in the past year

Rank #20,451 · ~7/day · ~220/mo

Releases R versions

Daily download trend is not available in this view yet.

17330 days

55590 days

2.6K1 year

Compare downloads with other packages →

Also on98 r2u

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (2)

R >= 3.5.0limma

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Lianbo Yu

Author, Maintainer

Authors (1)

Lianbo Yu

Author, Maintainer

Listed in earlier versions (1)

The Ohio State University

no longer listed · 1.0

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
2.0Latest
2022-09-05 · current release · diff ↗
unarchivedReturned to CRAN
2022-09-05
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
archivedRemoved from CRAN
2019-01-26
check problems were not corrected despite reminders
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10

Show 3 earlier events

R
R 3.0.0 released · 2013-04-03
1.0
2012-08-30
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-08-30
Total releases: 2 / 14 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Download size: 3.2 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("fmt")

Format

Yu, L. (2022). fmt: Variance Estimation of FMT Method (Fully Moderated T-Statistic) (Version 2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.fmt

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for fmt version 2.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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