Figure 2 : Sample-wise similarity between data obtained using various profiling platforms.

From: In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development

Figure 2

Pearson sample-wise correlation coefficients between gene expression levels (differential genes only are used with group t-test P value <0.05) obtained with Affymetrix and Agilent platforms for the same set of samples are shown in blue. Pearson sample-wise correlations between corresponding pathway activation values calculated using iPANDA are shown in yellow. Dashed and dotted lines represent, respectively, the median with upper and lower quartiles of the empirical distribution. Gene expression data was obtained from MicroArray Quality Control (MAQC) data set (GEO identifier GSE5350). Application of iPANDA leads to higher correlation between the data obtained using different experimental platforms for the same samples.