Figure 9

Comparison with respect to dChip, RMAExpress, and Expression Console. Each column represents the flow of information when using respectively dChip, RMAExpress, Expression Console, and μ-CS. At summarization-normalization layer, label a) indicates which preprocessing algorithms can be chosen. dChip and RMAExpress support only one algorithm, while the other tools include more algorithms, e.g. RMA and Plier. At the annotation layer, label b), all the tools, except for RMAExpress, supports annotation. dChip support annotation using user provided files, while Expression Console and μ-CS automatically download annotation files. Thus RMAExpress produces only preprocessed data, while the other tools produce preprocessed and annotated data. Finally at the analysis layer, label c), we note that data provided by dChip can only be analysed with dChip itself, while data provided by the other tools can be analysed by third parts softwares, and in particular by TMeV.