This is a follow up to my previous question.
I would like to implement the following steps given in the supplementary file of this study to reproduce the figure 1 displayed in the paper.
We used Affymetrix microarray data from a recent thorough analysis of the mouse and human transcriptomes . We selected all 54 adult mouse non-cancer samples. The raw intensity data were transformed to normalized expression levels with the robust multi-array average (RMA) lowlevel algorithm  implemented in the BioConductor package . We used standard settings, including perfect match (PM) only, model-based background and quantile normalization across experiments . Similar results were obtained using the microarray analysis suite (MAS5) function followed by log-transformation to calculate expression levels (data not shown).
Mouse data is available on GEO with access ion number GSE1133. The data is available in different formats like CDF, CIF, GIN, PSI, SIF, PROBE, TAB, TXT. I am not sure which data format, containing the raw intensity data, has to be downloaded for implementing the procedure described above.