ABSTRACT
We present a mathematical model to extend the dynamic range of gene expression data measured by laser scanners. The strategy is based on the rather simple but novel idea of producing two images with different scanner sensitivities, obtaining two different sets of expression values: the first is a low-sensitivity measure to obtain high expression values which would be saturated in a high-sensitivity measure; the second, by the converse strategy, obtains additional information about the low-expression levels. Two mathematical models based on linear and gamma curves are presented for relating the two measurements to each other and producing a coherent and extended range of values. The procedure minimizes the quantization relative error and avoids the collateral effects of saturation. Since most of the current scanner devices are able to adjust the saturation level, the strategy can be considered as a universal solution, and not dependent on the image processing software used for reading the DNA chip. Various tests have been performed, on both proprietary and public domain data sets, showing a reduction of the saturation and quantization effects, not achievable by other methods, with a more complete description of gene-expression data and with a reasonable computational complexity.
ABSTRACT
UNLABELLED: PreP is a versatile, powerful, standalone application that aims at pre-processing gene expression data. AVAILABILITY: Documentation and executable file for MS-Windows are available at http://chirimoyo.ac.uma.es/bitlab/services/index.htm
Subject(s)
Algorithms , Database Management Systems , Gene Expression Profiling/methods , Information Storage and Retrieval/methods , Sequence Analysis/methods , Software , User-Computer Interface , Programming LanguagesABSTRACT
Engene is a versatile, and platform-independent web tool for exploratory analysis of gene expression data that aims at storing, visualizing and processing large sets of gene expression patterns.
Subject(s)
Algorithms , Database Management Systems , Gene Expression Profiling/methods , Sequence Alignment/methods , Sequence Analysis, DNA/methods , Software , User-Computer Interface , Information Storage and Retrieval/methodsABSTRACT
The user-friendly MicroPreP framework was developed to transform raw intensity data from cDNA microarrays into high-quality data. The main features of this software are: LOWESS normalisation; merging of DNA microarray data from changing slide versions; outlier detection; and slide quality assessment.
