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arrayQualityMetrics

arrayQualityMetrics. B ioconductor package for: Affymetrix, Agilent, Illumina, homemade arrays etc... RNA, tiling, exon, SNP arrays, etc… From an R object → HTML report Plots: MA plot and spatial representations Boxplots and density Heatmap and PCA Variance-mean dependency

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arrayQualityMetrics

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  1. arrayQualityMetrics • Bioconductor package for: • Affymetrix, Agilent, Illumina, homemade arrays etc... • RNA, tiling, exon, SNP arrays, etc… • From an R object → HTML report • Plots: • MA plot and spatial representations • Boxplots and density • Heatmap and PCA • Variance-mean dependency • GC content and probe mapping studies • Affymetrix only: NUSE, RLE, RNA degradation, QCstats, PM/MM • Outlier identification

  2. Outlier detection • For each array i, where k is a probe and Mik is the log(ratio) of probe k on array i

  3. ArrayExpress database • ArrayExpress is a public repository for microarray data • Store MIAME-compliant data in accordance with MGED recommendations • http://www.ebi.ac.uk/microarray-as/aer • Content : • > 8000 experiments • 230 000 hybridizations available

  4. Bioconductor assayData phenoData featureData experimentData Data structure • MAGE-TAB raw.zip SDRF Sample and Data Relationship Format ADF Array Design Format IDF Investigation Description File Quantitation Types

  5. ArrayExpress package efficiency

  6. ArrayExpress content– Size of the experiments per year

  7. Outliers per year Array-Distance NUSE

  8. Outliers per Impact Factor Array-Distance NUSE

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