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Data were analyzed using the Affymetrix Microarray Suite 5.0.
All GEPs were performed using the Affymetrix microarray platform and standard procedures.
Gene Chips were scanned with an argon-ion laser and data visualized using the Affymetrix Microarray Suite 5.0 software.
In each cell line, we compared the expressions of 22.000 genes in vitro and in the xenografts, using the Affymetrix microarray approach.
To facilitate comparisons among microarrays, global scaling was performed using the Affymetrix Microarray software (MAS 5.0) and the target intensity was set to 500.
The GeneChips data analysis was performed using the Affymetrix Microarray suite 5 and the GeneSpring 5 (Agilent Technologies, Palo Alto, CA) analysis package.
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Both the Sequenom MassArray and 70-mer oligonucleotide microarray analyses indicate that the majority of the DE profiles identified using the Affymetrix microarrays were valid.
Annulus gene expression analysis used the Affymetrix microarray system.
These experiments all used the Affymetrix microarray platform.
For calculation of signal intensity of each gene we used the Affymetrix Microarray Suite 5.0 Software (MAS5).
Moreover, all the studies either determined the expression of preselected genes such as TLRs, MHC-II molecules, chemokines and cytokines by quantitative RT-PCR or used the Affymetrix microarray, so the measurements were limited to the level of transcription.
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