MDimNormn

Multi-Dimensional MA Normalization for Plate Effect

v0.8.0 · Aug 12, 2015 · GPL-3

Description

Normalize data to minimize the difference between sample plates (batch effects). For given data in a matrix and grouping variable (or plate), the function 'normn_MA' normalizes the data on MA coordinates. More details are in the citation. The primary method is 'Multi-MA'. Other fitting functions on MA coordinates can also be employed e.g. loess.

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CRAN Check Status

13 NOTE

Show all 13 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	21.1s
r-devel-linux-x86_64-debian-gcc	NOTE	17.8s
r-devel-linux-x86_64-fedora-clang	NOTE	32.8s
r-devel-linux-x86_64-fedora-gcc	NOTE	30.2s
r-devel-windows-x86_64	NOTE	39s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	NOTE	22s
r-oldrel-windows-x86_64	NOTE	36s
r-patched-linux-x86_64	NOTE	19.3s
r-release-linux-x86_64	NOTE
r-release-macos-arm64	NOTE	9s
r-release-macos-x86_64	NOTE	24s
r-release-windows-x86_64	NOTE	38s

Check details (15 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Mun-Gwan Hong <mun-gwan.hong@scilifelab.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mun-Gwan",
                    family = "Hong",
                    role = c("aut", "cre"),
                    email = "mun-gwan.hong@scilifelab.se")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-debian-clang

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Mun-Gwan Hong <mun-gwan.hong@scilifelab.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mun-Gwan",
                    family = "Hong",
                    role = c("aut", "cre"),
                    email = "mun-gwan.hong@scilifelab.se")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-debian-gcc

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Mun-Gwan Hong <mun-gwan.hong@scilifelab.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mun-Gwan",
                    family = "Hong",
                    role = c("aut", "cre"),
         
...[truncated]...
ifelab.se")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Mun-Gwan Hong <mun-gwan.hong@scilifelab.se>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mun-Gwan",
                    family = "Hong",
                    role = c("aut", "cre"),
         
...[truncated]...
ifelab.se")
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^

Version History

1 tracked

new 0.8.0 Mar 10, 2026

R Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN Aug 12, 2015. Releases before tracking aren’t shown.