Processing Pipeline for Microarray SPPs

From LipidomicsWiki

A processing pipeline for microarrays usually consists of two steps: First of all a feature extraction step which extracts intensities for features out of images produced by the scanner. Afterwards the user selects the arrays which should be loaded into a second program e.g. Chipinspector or R for further preprocessing and analysis (e.g.test for Differential Expression, Clustering). Therefore no fully automated pipeline was possible. But the intermediate selection step is usually very convenient.

The R script implementing the Preprocessing of Single Colored Agilent Arrays -SPP covers reading, preprocessing and transformation of microarray data. It was designed in a way that it needs a minimum of input by the user. Further analysis steps can  easily be added by users who are familiar with R. The R-script is available by request from the Institute for Clinical Chemistry in Regensburg.

The analysis by Chipinspector is made in a highly automated fashion and also requires only few input from the user.

Standard Processing Procedure

Microarray SPPs

Standing Processing Procedures Main Page

Implementation

Implementation of Microarray SPPs