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The bio-specimen collection criteria, sample processing, clinical data quality assurance and microarray processing had been described by TCGA previously [ 14].
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The methods used for microarray data processing have been described in detail previously [47].
Details on the microarray data processing have been previously described [ 57].
Microarray filtering and data processing has an important effect on the correlation coefficient results generated by each method.
Our study shows that microarray data normalization and processing have important effects on the final outcome, especially for the identification of differentially expressed genes.
Although some bioinformatic analysis has been performed in particular microarray assays [ 6, 7], an extensive data evaluation and processing has not yet been performed.
But speedier processing has some downsides.
Microarray processing and hybridization protocols have been described previously [ 36, 45].
Selection of an appropriate statistical method for microarray processing is a significant subject of scientific discussion and although microarrays have been in use for more than fifteen years, many issues related to data analysis remain unresolved.
Several recent articles have provided substantial evidence that systematic noise introduced as a result of batch-processing have a detrimental effect on data derived from microarrays [ 1- 5].
Microarray processing and the statistical methodology used to build and validate the signature is described in the Additional file 1.
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