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Microarrays measured gene expression by hybridising labelled RNA to spots of known DNA on a chip; they preceded RNA sequencing and still hold the longest-followed cohorts.
A DNA microarray is a collection of microscopic DNA spots on a solid surface used to measure the expression of large numbers of genes at once (Wikipedia). The METABRIC breast cancer cohort of about two thousand patients with long follow-up is microarray based, which makes it the standard external test for TCGA-trained RNA-seq survival models and a stern one: intensities and read counts have different distributions, so a model must be rank- or quantile-normalised to cross platforms.
Shares Quantile normalisation, rank transforms and z-scores, Batch effects and harmonisation, Bulk RNA sequencing (RNA-seq) and the full transcriptome, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Quantile normalisation, rank transforms and z-scores, Batch effects and harmonisation, External validation, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Batch effects and harmonisation, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Bulk RNA sequencing (RNA-seq) and the full transcriptome, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Bulk RNA sequencing (RNA-seq) and the full transcriptome, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares External validation, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares External validation, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares External validation, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.