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In two cases, the samples were annotated as male but clustered within the females; these are likely mis-annotations.
Samples were annotated to the four subtypes (neural, proneural, mesenchymal and classical) defined by Verhaak et al.,27 using a supervised approach based on support vector machines (SVM).
An additional 30 of the genes with higher expression in the neo aortic samples were annotated to Wnt receptor signaling pathway, which was the term ranked in third place by MGSA.
Firstly, the SNPs/InDels detected in the samples were annotated.
The samples were annotated with an anonymous but traceable barcode.
Of the 98 cores stained, 81 breast cancer samples were annotated for patient survival data.
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The samples are annotated in Additional file 1, Table S1.
Two other upregulated genes in our constitutive samples are annotated as putative phenylcoumaran benzylic ether reductase.
Discordance in the direction of the G-gap between the two samples is annotated by a negative product (see research design and methods ).
This data matrix has dimensions 5000 CpGs (the 5000 most variable positions) by 134 samples; samples are annotated according to whether they are HOTAIR + ve/-ve and type of chemotherapy received.
MIAME was originally designed to provide standards for microarray data sharing to ensure that " data can be easily interpreted and that results from its analysis can be independently verified" [ 24]; GEO requires that both raw and normalized data be available, samples are annotated (including experimental design) and laboratory and data processing protocols are described.
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