My Microarray Software Comparison - Data Preprocessing Software

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Definition of data preprocessing software
Data preprocessing software (in alphabetical order)

[ Data munging tools | Excel | Gene Expression Pattern Preprocessor | Mergem | Microhelper | MIDAS ]

Definition of data preprocessing software

Data preprocessing software (in alphabetical order)

• Data munging tools - A number of data munging tools for microarray data. All have perl/tk graphical user interfaces, written by Charlie Kim at Falkow Lab, Stanford University.
• Excel - can handle/ generate larger tab-delimited text files, very useful tool for manipulating raw data.
• Gene Expression Pattern Preprocessor - a web-based tool and it performs scale transformation, replicate handling, missing value imputation, flat pattern filtering and pattern normalisation, written by Bioinformatics Unit  of CNIO. There is alsoa Pre-analyse module which performs several checks and plots several histograms to help and to guide the user through the options. The final result can be automatically sent to their local analysis tools and to the EBI EPCLUST. Reference [PubMed]
  
• Mergem  - a perl utility for merging big data files by UC Irvine; you can also use their web interface to do so if you hate UNIX
• Microhelper 1.02 - a tool for merging, filter, normalize, transform, handle missing, select subset, remove control and annotate data, written by Chang Bioscience
• MIDAS (Microarray Data Analysis System) - TIGR Microarray Data Analysis System (MIDAS) is a microarray data quality filtering and normalization tool that allows raw experimental data to be processed through various data normalizations, filters, and transformations via a user-designed analysis pipeline. MIDAS is implemented by Java language. It requires JDK v1.3.1 or higher. MIDAS is written by The Institute of Genomic Research (TIGR). Reference [PubMed]