Microarray SPPs

From LipidomicsWiki

Contents 1 Introduction 2 SPPs for Agilent platform 3 Ensembl genes for which no Agilent Probe ID can be found 4 SPPs for Affymetrix platform 5 Implementation 6 Processing Pipeline

Introduction

Microarray processing contains several different steps. After hybridization usually an image is taken with a suitable scanner. The raw intensities of the different features have to be computed out of this images. Preprocessing steps like background correction, normalization and finally analysis (significance tests, clustering) may be executed.
Intensity extraction, background correction and flagging is done by the agilent feature extractor.( See Agilent Feature Extraction ) After Feature Extraction ChipInspector can be used for detection of differential expression. It performs normalization as well as differential expression (see SPP Differential_Expression_with_ChipInspector ). The ChipInspector will be one of the main tools for differential expression at the Institute for Clinical Chemistry in Regensburg.

Normalization and analysis-steps like significance tests and clustering may also be executed by other analysis programms like R.  Preprocessing of Single Colored Agilent Arrays contains the default normalization settings for one-colored agilent arrays in Genespring. This settings can be used as a basis for a R-pipeline. Further analysis steps like significance-tests and clustering besides ChipInspector will not be covered, since they depend on the kind of experiment performed.

We focussed in our SPPs on Agilent processing, since this is the main Microarray-platform at LipidomicNet. 

SPPs for Agilent platform

• Agilent Feature Extraction
• Preprocessing of Single Colored Agilent Arrays
• Differential Expression with ChipInspector
• Differential Expression using the B-Fabric Analysis tool
  

Ensembl genes for which no Agilent Probe ID can be found

You can find a list here.

SPPs for Affymetrix platform

• Preprocessing and differential expression with CARMAWeb

Implementation

Implementation of Microarray SPPs

Processing Pipeline

Processing Pipeline for Microarray SPPs

Back to Standard Processing Procedures Main Page