Limma (analysis)

Analysis title

Limma

Provider

geneXplain GmbH

Class

LimmaComparator

Plugin

com.genexplain.analyses (geneXplain analyses)

Estimate differential expression using Linear Models for MicroArrays (LIMMA)

Parameters

• Input table - Table with normalized measurement values
• Input log-base - Logarithmic base of input data
• 1. Condition / group name - Name for first condition / group
• 1. Columns - Columns assigned to first condition / group
• 2. Condition / group name - Name for second condition / group
• 2. Columns - Columns assigned to second condition / group
• 3. Condition / group name - Name for third condition / group
• 3. Columns - Columns assigned to third condition / group
• 4. Condition / group name - Name for fourth condition / group
• 4. Columns - Columns assigned to fourth condition / group
• 5. Condition / group name - Name for fifth condition / group
• 5. Columns - Columns assigned to fifth condition / group
• Output folder - Folder to store output tables

Please not that the first two groups (named Treatment and Control by default) are not optional and unnamed groups are not considered.

Output

The output contains the columns described below. Columns highlighted in bold are shown in the default view. The other columns can be included on demand via the Columns tab of the lower right panel (available with opened output table).

logFC

Fold change (log)

CI.025

Fold change (Lower confidence interval)

CI.975

Fold change (Upper confidence interval)

AveExpr

Average log2-expression for the probe over all arrays

t

Moderated T-statistic

P.Value

P-value Differential expression

adj.P.Val

Adjusted P-value (Benjamini-Hochberg)

B

Log-odds that the gene / probe shows differential expression

modLog10P

Modulus of the decadic P-value logarithm

signLog10P

Decadic P-value logarithm with same sign as the log fold change

Description

Limma estimates differential expression between specified conditions / groups.

This tool provides an interface for the popular and comprehensive Limma package. The platform tool computes differential expression between up to five conditions / groups. The groups consist of columns of a data table that contains normalized measurement values, e.g. from a normalized microarry experiment. All possible contrasts between groups are considered and their output is stored in a common folder. Conditions are compared in the specified order from first to fifth. E.g. given conditions named A, B and C, the output will contain the contrasts AvsB, AvsC and BvsC.

It is necessary to provide a unique name for each group. Also, at least two data columns are required per group.

Reference

Smyth, G. K. (2005). Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, 2005.