Pre-Processing & Quality Control of Raw Data

  • Quality assessment is conducted by detailed microarray image analysis to identify scanning artefacts, as well as raw intensity data checks
  • Pre-processing includes background signal correction, intra- and inter-array normalization, as well as feature summarization
  • Additional quality checks are performed for the pre-processed data to ensure high quality results. Measures such as sample correlation, hierarchical clustering of samples, as well as principal component analysis (PCA) are used to assess sample relations

mRNA/miRNA Microarray Analysis

  • Annotation of probes/transcripts/genes with available meta-information
  • Identification of differentially expressed probes/transcripts/genes
    • Variation and fold-change analysis for predefined sample groups
    • Statistical assessment of differences in expression, including ANOVA, t-test or non-parametric statistics, as well as multiple testing correction
  • Time Series Data Analysis
    • Statistical assessment of differences between time points
    • Visualization of time series data
  • Data Mining
    • Supervised or unsupervised clustering as well as cluster quality assessment
    • Gene mining
  • Gene Ontology (GO) Enrichment Analysis
    • Annotation of probes/transcripts/genes with GO IDs and terms
    • Statistical evaluation of overrepresented GO terms
    • Visualization of overrepresented GO group hierarchies
  • Ingenuity based Pathway Analysis (IPA)
    • Identification of canonical pathways
    • Upstream regulator analysis
    • Analysis of biofunction and impact on disease
  • Data delivery
    • Raw array data, e.g. CEL files for Affymetrix® gene chips
    • Quality control data package, including diagnostic plots and statistics in text-based format
    • Lists of differentially expressed probes/transcripts/genes in text-based format
    • Data package for data mining applications, including lists of probes/transcripts/genes as well as high quality visualizations
    • Data package for GO enrichment analyses, including lists of differentially expressed probes/transcripts/genes contained in enriched GO categories
    • Data package for pathway analysis including gene lists and visualizations of biologically significant results
    • For each analysis a report in PDF format is provided with detailed information on the different analysis steps, tools used in the processing and results from the applied methods

Genotyping Microarray Analysis

  • Pre-processing includes background signal correction, removal of variation, normalization steps, as well as probe set summarization
  • Additional quality checks are performed for the pre-processed data to ensure high quality results.
  • Detection of copy number variations
  • Detection of LOH (Loss of Heterozygocity)
  • Genotyping
    • Genotyping calls
    • Linkage Analysis
    • Association study
  • Data delivery
    • Raw array data, e.g. CEL files
    • Pre-calculated CYHD.files
    • Lists of copy number changes in PDF format
    • Lists of LOH reports in PDF format
    • Table of genotyping results in text-based format
    • Table of linkage results in text-based format
    • Table of association results in text-based format