Compute differentially expressed genes using EBarrays (workflow)

Workflow title

Compute differentially expressed genes using EBarrays

Provider

geneXplain GmbH

Workflow overview

Description

This workflow is designed to identify differentially expressed genes from several experimental conditions applying EBarrays statistics. Normalized data can be generated from Affymetrix (normalization/Affymetrix normalization Affymetrix normalization), Agilent (normalization/Agilent normalization Agilent normalization) or Illumina (normalization/Illumina normalization Illumina normalization) raw data and submitted as input. Please note that the EBarray method requires two or more replicates for each condition.

The workflow compares up to five conditions / groups in one run. One control group is needed to run this workflow and you need to specify at least two conditions (e.g. "control group" and "disease group"). All possible comparisons between the input groups are calculated in one workflow run. The first step of the workflow is a quality control of the input data and gives out a density boxplot and a density plot. The primary result of the EBarray method is filtered by several conditions in parallel, applying the Filter table method to identify up- and down-regulated probeset IDs for each comparision.

For up-regulated probes: LogFoldChange>0.5 and Sig ==1.

For down- regulated probes: LogFoldChange<-0.5 and Sig ==1.

The tables with filtered up- and down-regulated genes are then annotated with a gene description and a gene symbol.

The output folder contains gene tables as well as the images of the density boxplots and density plots.

Reference: Kendziorski, C.M., Newton, M.A., Lan, H., Gould, M.N. (2003). On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Statistics in Medicine 22:3899-3914.

Parameters

Input table

Input table with all normalized files

Probe type

Species

Control group

Enter control name without spaces

Control_columns

Select columns for control

group_2

Enter Condition 2 name without spaces

Columns_group_2

Select columns for condition 2

group_3

Enter Condition 3 name without spaces

Columns_group_3

Select columns for condition 3

group_4

Enter Condition 4 name without spaces

Columns_group_4

Select columns for condition 4

group_5

Enter Condition 5 name without spaces

Columns_group_5

Select columns for condition 5

Results folder