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Extended data analysis using DeCyder EDA

ser license 28-4012-03

DeCyder 2-D Differential Analysis Software v6.5, preinstalled network 28-4012-01
(including PC and single concurrent network user license)


Analysis
Original data set
The original data set was a BVA workspace from a study on human ovarian cancer. All samples were classified by pathologists into one of the following three groups: normal, benign, or malignant. A subset of samples from 18 patients (three normal, four benign, 11 malignant) was run in duplicate and used to perform all subsequent analysis. For the classifier, nine (one as duplicate) “unknown” patients were used to verify the analysis, as well as the classification made by the pathologists.

Workspace
We created our EDA workspace by importing the BVA workspace from the cancer study. No statistical values from the BVA workspace were copied into the EDA workspace. Standard spot maps from the master and matched gels (to provide matching information) were copied into the EDA workspace but were not included in the actual analysis.

Experimental design
In the BVA workspace we imported, an experimental design was already defined. This was transferred to the EDA workspace.

Base set creation
The starting material (biopsy tissue) had a large variation, from both the inherent biological variation and the sample preparation. This led to a situation where only a small number of proteins was present in all spot maps or not matched.

For our cancer study we decided to filter out unassigned spot maps (master image and other spot maps not assigned to given groups), as well as proteins present in less than 80% of the spot maps. The remaining spot maps and proteins comprised
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