Component: ExprMixtureModel

ExprMixtureModel

Provides a mixture model fit of two normal distributions for the given genes. Each gene is processed individually.

Output columns:

gene

identifier of the expression profile

normality

P-value of associated with the Shapiro-Wilk normality test

loglik

log likelihood of the mixture model

m1mean

mean of the first Gaussian component

m2mean

mean of the second Gaussian component

m1sd

standard deviation of the first Gaussian component

m2sd

standard deviation of the second Gaussian component

m1prop

proportion of samples captured by the first Gaussian component

m2prop

proportion of samples captured by the second Gaussian component

selected

expression profile satisfies the given thresholds and is plotted

normalized mutual information score

Version	1.4
Bundle	microarray
Categories	DEG Quality Control
Authors	Marko Laakso (Marko.Laakso@Helsinki.FI), Mikko Kivelä (bolozna@gmail.com)
Issue tracker	View/Report issues
Requires	R ; mixtools (R-package)
Source files	component.xml ExprMixtureModel.r
Usage	Example with default values ExprMixtureModel( expr = Matrix, //annot = AnnotationTable, //groups = SetList, annotCols = "", group1 = "", group2 = "", maxLoglik = -800, maxOverlap = 1.00, minDifference = 2.0, minInfo = 0.0, minProportion = 0.2, sdPoint = 2.0, sectionTitle = "Gene expression mixture model", sectionType = "subsection", showIfFail = true )

Version

1.4

Bundle

microarray

Categories

DEG Quality Control

Authors

Marko Laakso (Marko.Laakso@Helsinki.FI), Mikko Kivelä (bolozna@gmail.com)

Issue tracker

View/Report issues

Requires

R ; mixtools (R-package)

Source files

component.xml ExprMixtureModel.r

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
expr	Matrix	Mandatory	Expression matrix
annot	AnnotationTable	Optional	Gene names and other related annotations
groups	SetList	Optional	Sample groups

Name

Type

Mandatory

Description

expr

Matrix

Mandatory

Expression matrix

annot

AnnotationTable

Optional

Gene names and other related annotations

groups

SetList

Optional

Sample groups

Outputs

Name	Type	Description
stats	AnnotationTable	Distribution statistics for all input genes
report	Latex	Distribution plots for the selected genes
samplesets	Matrix	Samples associated with the model components. Provides the posterior probabilities for each sample to belong to the first components.

Name

Type

Description

stats

AnnotationTable

Distribution statistics for all input genes

report

Latex

Distribution plots for the selected genes

samplesets

Matrix

Samples associated with the model components. Provides the posterior probabilities for each sample to belong to the first components.

Parameters

Name	Type	Default	Description
annotCols	string	""	A comma separated list of gene annotation column names to be shown
group1	string	""	ID of the first sample group or an empty string for the first group within the groups input
group2	string	""	ID of the second sample group or an empty string for the second group within the groups input
maxLoglik	float	-800	Maximum of the log likelihood for the mixture model
maxOverlap	float	1.00	Maximum overlap between the distribution components
minDifference	float	2.0	The difference of the distribution component means is at least this many times the standard deviation of the less variatiating distribution.
minInfo	float	0.0	Minimum for the normalized mutual information score when groups 1 and 2 are defined.
minProportion	float	0.2	The smaller distribution component should cover at least this proportion of the samples.
sdPoint	float	2.0	Cut-off points are visualized at (+,-)sdPoint*mean.
sectionTitle	string	"Gene expression mixture model"	If non-empty, a declaration of a new section with the given name is inserted to the beginning of the combined document.
sectionType	string	"subsection"	Type of LaTeX section: usually one of section, subsection or subsubsection. No section statement is written if sectionTitle is empty.
showIfFail	boolean	true	Show distributions where the model fit algorithm has failed

Name

Type

Default

Description

annotCols

string

A comma separated list of gene annotation column names to be shown

group1

string

ID of the first sample group or an empty string for the first group within the groups input

group2

string

ID of the second sample group or an empty string for the second group within the groups input

maxLoglik

float

-800

Maximum of the log likelihood for the mixture model

maxOverlap

float

1.00

Maximum overlap between the distribution components

minDifference

float

2.0

The difference of the distribution component means is at least this many times the standard deviation of the less variatiating distribution.

minInfo

float

0.0

Minimum for the normalized mutual information score when groups 1 and 2 are defined.

minProportion

float

0.2

The smaller distribution component should cover at least this proportion of the samples.

sdPoint

float

2.0

Cut-off points are visualized at (+,-)sdPoint*mean.

sectionTitle

string

"Gene expression mixture model"

If non-empty, a declaration of a new section with the given name is inserted to the beginning of the combined document.

sectionType

string

"subsection"

Type of LaTeX section: usually one of section, subsection or subsubsection. No section statement is written if sectionTitle is empty.

showIfFail

boolean

true

Show distributions where the model fit algorithm has failed

Test cases

Test case	Parameters▼	IN expr	IN annot	IN groups	OUT stats	OUT report	OUT samplesets
case1	properties	expr	annot	groups	stats	report	samplesets
	annotCols = name,description, group1 = case, group2 = control
case2	properties	expr	(missing)	(missing)	stats	report	samplesets
	showIfFail = false, maxLoglik = 0.0

Test case

Parameters▼

IN
expr

IN
annot

IN
groups

OUT
stats

OUT
report

OUT
samplesets

case1

properties

expr

annot