wiki:DIGEAnalyzer

DIGE Analyzer

The effects of protein-specific dye-effects should be taken into account when analyzing sets of DiGE gels for optimal results. The method described by Krogh et al in Proteomics 2007 has been integrated into Proteios. The analysis software is described at the DIGEanalyzer home page.

Proteios provides conversion of Decyder BVA XML files to the DIGEanalyzer input format. Upload the BVA file to your Proteios server. Then check the check box and select Extensions->Convert file[s]->Decyder BVA to DIGE Analyzer converter. A .txt file with the same name as the XML file will be written to the same directory as the BVA XML was found in.

The conversion plugin will look for grouping information if it has been entered for the samples that were used for the gels. To ensure this, you should upload the gel images and add the sample tracking information from samples -> extracts -> labeled extract-> separations -> scanning. The top level sample and extract should be annotated with the annotation "group". This group annotation is added to the DIGE analyzer .txt file by the conversion plugin. If it cannot be found, the group information is instead retained from the Decyder BVA file.

In the case of large projects you may need to divide the BVA project into several sub-groups before exporting the XML. In this case, all the sub-groups should have the same master gel. Then run the conversion plugin on all the XML files. Finally, check all the generated .txt files and select Extensions->Merge DIGE analyzer files to one. A new file named merged...txt will be written.

To run the actual analysis, select the .txt file from the above procedure and select Extensions->Run analysis plugin->DIGE analyzer. A tab separated file with the result will be written.

Last modified 13 years ago Last modified on Sep 18, 2008, 4:10:23 PM