Table 1. Summary of the processing methods recommended for different levels of data.
Data Type | Analysis Task | Recommended Approach |
All levels | Quality assessment | Examine scanner metrics |
Rawa | Local background adjustment | Median background subtraction |
Raw | Transformation | log2 |
Bead-levelb | Spatial artefact detection & removal | BASH |
Bead-level | Quality assessment | Examine image plots & boxplots |
Bead-level | Summarization | Default Illumina method |
Summary-levelc | Data export from BeadStudio/ GenomeStudio | Non background corrected, non normalized, Sample and Control “Probe Profile” tables |
Summary-level | Quality assessment | Examine boxplots of regular & control probes, MDS plots |
Summary-level | Background correction | Normal-exponential convolution using negative controls |
Summary-level | Normalization | Quantile |
Summary-level | Transformation | log2 |
Summary-level | Estimation of proportion of expressed probes in a sample | Mixture model that uses negative controls (propexpr [29]) |
Summary-level | Probe filtering | Based on annotation quality |
Summary-level | Differential expression analysis | Linear modelling using weights |
Raw data comprises one observation per pixel, per array.
Bead-level data comprises one observation per bead, per array.
Summary-level data comprises one observation per probe type, per sample.