Component: SVDAnalyzer

SVDAnalyzer

Performs Singular Value Decomposition to gene sets to test whether a set of genes is significantly differentially expressed.

In the SVD method the expression values of multiple variables (=genes) are captured into one variable called metagene. This metagene is the main component of the SVD and captures most of the variation in the expression matrix.

The main idea of SVDAnalyzer is to summarize the expression values of a sample in a gene set into a single value called activity level. The activity level is defined for each sample in each pathway by using SVD. The activity level can be regarded as a weighted sum of the expression values, where the weights are given by the first metagene.

The activity levels are, then, used to make comparisons between the sample groups. These comparisons can be made by calculating e.g. t statistic for each pathway.

Required packages

Install package 'genefilter' from R: source('http://bioconductor.org/biocLite.R'); biocLite(); Install package 'csbl.go' from CSBL pages: csbl.go (requires package RUnit) Install package 'Category' from R: biocLite('Category');

Version	1.0
Bundle	microarray
Categories	Analysis Pathway
Authors	Minna Miettinen (Minna.Miettinen@Helsinki.FI)
Issue tracker	View/Report issues
Requires	R ; libxml2-dev (DEB) ; MASS (R-package) ; KEGG.db (R-bioconductor) ; genefilter (R-bioconductor) ; csbl.go (R-package) ; Category (R-bioconductor)
Source files	component.xml analyzer.R
Usage	Example with default values SVDAnalyzer( annotation = CSV, expr = LogMatrix, sampleGroupTable = SampleGroupTable, database = "GO", group1 = "", group2 = "", nPath = 50, nperm = 10000, pPlots = 0.01, pagebreak = false, section = "", sectionType = "subsection", seed = 12345, sourceId = "GeneId", targetId = "GeneSetId", threshold = 10 )

Version

1.0

Bundle

microarray

Categories

Analysis Pathway

Authors

Minna Miettinen (Minna.Miettinen@Helsinki.FI)

Issue tracker

View/Report issues

Requires

R ; libxml2-dev (DEB) ; MASS (R-package) ; KEGG.db (R-bioconductor) ; genefilter (R-bioconductor) ; csbl.go (R-package) ; Category (R-bioconductor)

Source files

component.xml analyzer.R

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
annotation	CSV	Mandatory	Gene annotation table. Parameters sourceId and targetId specify the columns containing the names of the genes and respective annotations.
expr	LogMatrix	Mandatory	The expression values of the genes. First column should contain the same gene identifiers as the sourceId column in the annotation table. The number of rows i.e. genes, can be more than the number of sourceIds in the annotation table. However, expression values for all the sourceIds should be found in the expr table.
sampleGroupTable	SampleGroupTable	Mandatory	SampleGroupTable represents the relation between a sample and its group. Table should contain at least two groups. The activity levels are determined by performing SVD using expression data from all samples. However, only two groups can be selected to make comparisons with t-test. These groups are selected with parameters Group1, and Group2.

Name

Type

Mandatory

Description

annotation

CSV

Mandatory

Gene annotation table. Parameters sourceId and targetId specify the columns containing the names of the genes and respective annotations.

expr

LogMatrix

Mandatory

The expression values of the genes. First column should contain the same gene identifiers as the sourceId column in the annotation table. The number of rows i.e. genes, can be more than the number of sourceIds in the annotation table. However, expression values for all the sourceIds should be found in the expr table.

sampleGroupTable

SampleGroupTable

Mandatory

SampleGroupTable represents the relation between a sample and its group. Table should contain at least two groups. The activity levels are determined by performing SVD using expression data from all samples. However, only two groups can be selected to make comparisons with t-test. These groups are selected with parameters Group1, and Group2.

Outputs

Name	Type	Description
report	Latex	Latex report of the SVD results: activity level plots of interesting gene sets and a table presenting statistics for each gene set.
resultTable	CSV	Table presents analysis results in ascending order according to permuted p-value.

Name

Type

Description

report

Latex

Latex report of the SVD results: activity level plots of interesting gene sets and a table presenting statistics for each gene set.

resultTable

CSV

Table presents analysis results in ascending order according to permuted p-value.

Parameters

Name	Type	Default	Description
database	string	"GO"	The gene set identifiers used. The possible choices are "GO", "KEGG" or "other".
group1	string	""	The group whose expressions will be compared against Group2.
group2	string	""	The group whose expressions will be compared against Group1.
nPath	int	50	The number of top pathways presented in the latex report.
nperm	int	10000	The number of permutations produced while evaluating p value for a pathway.
pPlots	float	0.01	The pathways to be plotted. The activity levels of pathways with the p values smaller than Pplots are plotted. An error might occur if too high value is chosen for Pplots.
pagebreak	boolean	false	Tells if the resulting document should start with a page break.
section	string	""	Section title for the table container or an empty string in case no section is selected to be generated.
sectionType	string	"subsection"	Type of LaTeX section: usually one of: section, subsection, or subsubsection. No section statement is written if section title is empty.
seed	int	12345	Seed number for the pseudo random number generator
sourceId	string	"GeneId"	Character string specifying the column of gene identifiers in the input annotation.
targetId	string	"GeneSetId"	Character string specifying the column of gene set identifiers in the input annotation.
threshold	int	10	The minimum number of genes in a gene set.

Name

Type

Default

Description

database

string

"GO"

The gene set identifiers used. The possible choices are "GO", "KEGG" or "other".

group1

string

The group whose expressions will be compared against Group2.

group2

string

The group whose expressions will be compared against Group1.

nPath

int

The number of top pathways presented in the latex report.

nperm

int

10000

The number of permutations produced while evaluating p value for a pathway.

pPlots

float

0.01

The pathways to be plotted. The activity levels of pathways with the p values smaller than Pplots are plotted. An error might occur if too high value is chosen for Pplots.

pagebreak

boolean

false

Tells if the resulting document should start with a page break.

section

string

Section title for the table container or an empty string in case no section is selected to be generated.

sectionType

string

"subsection"

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

seed

int

12345

Seed number for the pseudo random number generator

sourceId

string

"GeneId"

Character string specifying the column of gene identifiers in the input annotation.

targetId

string

"GeneSetId"

Character string specifying the column of gene set identifiers in the input annotation.

threshold

int

The minimum number of genes in a gene set.

Test cases

Test case	Parameters▼	IN annotation	IN expr	IN sampleGroupTable	OUT report	OUT resultTable
case1	properties	annotation	expr	sampleGroupTable	report	resultTable
	group1 = low, group2 = high
case2	properties	annotation	expr	sampleGroupTable	report	resultTable
	pPlots = 0.01, group1 = trans, group2 = normal,
case3	properties	annotation	expr	sampleGroupTable	report	resultTable
	pPlots = 0.01 , database = KEGG, group1 = N, group2 = C, threshold = 1, seed = 35726, nPath = 20
case4	properties	annotation	expr	sampleGroupTable	report	resultTable
	database = KEGG, nperm = 500, sourceId = Uniprot, targetId = Pathways, threshold = 3, group1 = low, group2 = high

Test case

Parameters▼

IN
annotation

IN
expr

IN
sampleGroupTable

OUT
report

OUT
resultTable

case1