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Bioinformatics Vol. 18 no. 8 2002
Pages 1139-1140
© 2002 Oxford University Press

Applications Note

MArray: analysing single, replicated or reversed microarray experiments

Junbai Wang *, Vigdis Nygaard , Birgitte Smith-Sørensen , Eivind Hovig and Ola Myklebost

Department of Tumour Biology, Norwegian Radium Hospital, N0310 Oslo, Norway

Received on December 21, 2001 ; revised on February 14, 2002 ; accepted on March 1, 2002

Summary: 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

Contact: junbaiw{at}radium.uio.no

* To whom correspondence should be addressed.


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