Analysis Report


Sample


Data Preprocessing

  • All data processing was done using Bioconductor or APT tools

  • The offset of 1 was added to the origianl value before taking the log2

  • 'normgene' and 'control' genes were removed

  • Endpoint: data matrix of 876 genes X 16 samples

  • Download Processed Data


Quality Assessment

    Quality Assessment Report includes the following figures: Intensity Distribution, Mean Signal, BAC Spike, polya Spike, Pos Vs Neg Auc, Mad Residual Signal, RLE MEAN, and Hierarchical Clustering of Samples plots


Filtering

  • Probes with log2 intensity < 4 in more than 14 arrays are considered uninformative and removed

  • Probes with IQR < 10 % are considered uninformative and removed

  • After filtering: 763 probesets are left

  • Download Filtered Data


Identification of Differentially Expressed Genes

    mainEffect Comparison Adjusting Ratio P MultCompAdjtmt StatMethod Results
    Treatment Treated vs. Control none log2(1.5) 0.05 none limma 24 genes
    Treatment Treated vs. Control Group log2(1.5) 0.05 none limma 25 genes

    Treatment-X-Group

    Comparison Levels Ratio P MultCompAdjtmt StatMethod Results
    Treatment X Group none log2(1.5) 0.05 none limma 42
    Treated vs. Control A log2(1.5) 0.05 none limma 0
    Treated vs. Control B log2(1.5) 0.05 none limma 0