MArray: analysing single, replicated or reversed microarray experiments.

Junbai Wang; Vigdis Nygaard; Birgitte Smith-Sørensen; Eivind Hovig; Ola Myklebost

doi:10.1093/bioinformatics/18.8.1139

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MArray: analysing single, replicated or reversed microarray experiments.

Junbai Wang·Vigdis Nygaard·Birgitte Smith-Sørensen·Eivind Hovig·Ola Myklebost

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Abstract

UNLABELLED: MArray is a Matlab toolbox with a graphical user interface that allows the user to analyse single or paired microarray datasets by direct input of the raw data output file from image analysis packages, such as QuantArray or GenePiX. The application provides simple procedures to manually evaluate the quality of each measurement, multiple approaches to both ratio normalization (simple normalization, intensity dependent normalization) and evaluation of the reproducibility of paired experiments (using the techniques 'simple statistical method' and 'quality control ellipse' and 'significance analysis of microarrays'). Specifically, interactive spot evaluation functions are available in MArray and an online gene information database (NCBI UniGene) is linked. The application may provide a valuable aid in selecting and optimizing experimental procedures, as well as serving as an analytical tool for two-state biological comparisons, such as a study of single-dose activation. It is entirely platform independent, and only requires Matlab installed. AVAILABILITY: http://matrise.uio.no/marray/marray.html

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Computer Graphics DNA Database Management Systems Databases, Nucleic Acid Image Processing, Computer-Assisted Information Storage and Retrieval Models, Statistical Oligonucleotide Array Sequence Analysis Quality Control Reproducibility of Results Sensitivity and Specificity Software Statistics as Topic User-Computer Interface Journal Article Research Support, Non-U.S. Gov't

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Junbai Wang, Vigdis Nygaard, Birgitte Smith-Sørensen, Eivind Hovig, Ola Myklebost. 2002. MArray: analysing single, replicated or reversed microarray experiments.. https://doi.org/10.1093/bioinformatics%2F18.8.1139

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