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In conclusion, the study demonstrates the high diversity of gene expression profiles associated with melanoma, the necessity to include a sufficient number of samples regarding clinical standards, for the design of standardized sample collecting and preparation, for the development of common standards for microarray data processing, and for developing standardized bioinformatic tools.
Notably, no fully acceptable protocol exists for microarray data processing, and the different methods used for subsequent stages of the analysis pipeline may result in substantially different results.
For microarray data processing and normalization, microarray chips were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA) and median spot intensities were generated using GenePix 5.0 (Axon Instruments, Union City, CA).
DH and YL participated in microarray data processing and interpretation.
LS helped with microarray data processing and general statistical issues.
HW, SQ and LQB performed and contributed to the microarray data processing and analysis.
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RAI participated in the design of experiments, supervised data analysis, and provided expertise in DNA microarrays data processing and statistical analysis software.
WSB participated in the in-life study and microarray data processing.
CG and RT contributed to microarray data processing.
The microarray data processing protocol is described in the Supplementary Materials and Methods.
MZ and LW contributed to the evaluation of microarray data processing techniques.
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