GeExporter

Microarrays are often used to perform gene expression studies. Affymetrix provides the hardware (e.g. fluidics station, scanner etc.) the used microarrays and various software tools to control the hybridization process and to analyze the data generated by such an experiment. For example, the Microarray Suite (MAS) is used to perform and control the hybridization as well to preprocess the data, i.e. image processing, background subtraction, normalization and aggregation which are subsumed under MAS transformation. In contrast to Microarray Suite, the Data Mining Tool (DMT) can be used to analyse the data prepared by the MAS. To manage the data, Affymetrix provides the MicroDb which allows to store, archive, backup, restore etc. the data prepared by the MAS.

In our experience, Affymetrix MicroDb has some limitations. It only can store data of at most 128 hybridizations. If data for more than this number is produced, e.g. by the pair-wise comparison algorithm, different MicroDb's has to be used. Due to a cross-database comparison is not possible, often the same data are loaded into different MicroDb's. This could lead to several difficulties if a gene expression matrix has to be produced using data from multiple MicroDb's.

Therefore we have designed an application which simultaneously exports expression data of multiple hybridizations available in different MicroDb's to a files. Such a generated file can be a flat file (in Figure 1 named as GeWare format) or a gene expression matrix. GeExporter uses the Affymetrix analysis names to identify unique and duplicate hybridization data between the selected MicroDBs. For duplicate hybridizations, GeExporter allows the user to select a single one for export. Due to multiple transformed data can be derived from the same microarray, e.g. by applying different preprocessing algorithms, different parameters or applying different mask files, the user has to specify the corresponding chip name.

Figure 1 shows the screen of GeExporter to manage the data export. First, the user, has to select on the right top the necessary MicroDb's from whose the Affymetrix analysis are loaded. The top table comprises all unique Affymetrix analysis, th bottom table all duplicates. After selecting the analyses which should be exported the expression attributes as well as the file name can be specified.
Figure 1: GeExporter for expression export of multiple Affymetrix MicroDb's

The program is fully written in Java.

We hope this program is useful. Please, let us know, if you have any questions or recommendations to improve this program in the future.

We provide the binaries and the source code on request.


Last modified: 01.02.2004 by Toralf Kirsten

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