Fig. 3

Robust gene expression measurement across platforms following batch correction. Correction of systematic platform bias and integration of data from fresh frozen and FFPE tissues. a 3D multi-dimensional scaling (MDS) before (left) and after (right) batch correction of 6844 common genes. Samples coloured by platform and shapes indicates time point. b MDS plot of the batch corrected data with samples coloured by time-point clearly demonstrates a consistent treatment effect seen across sequential patient-matched samples. c Ultrasound measurements of the eleven breast tumours which relate to the sequential patient-matched samples indicating consistent reductions in tumour volume over time across the patients. d Ranking patient samples by the expression of 42 common proliferation genes (listed in Additional file 2: Table S2) illustrates consistent changes resulting from endocrine therapy, which appears to be independent from profiling platform. Pre-treatment samples tend to have relatively high proliferation, whilst as expected early, and particularly late on-treatment samples have lower proliferation. Heatmap colours are Red = High, Green = low