Table 1 List of CNV analysis software
Software | CN | locus-level CN (LRR = Log2R)†| Normalization (default target distribution) | Genomic-wave or GC correction | Batch-effect removal |
|---|---|---|---|---|---|
PennCNV | Relative | *R = (A + B)/ Rexp | Quantile (HapMap) | - | - |
Aroma.Affymetrix | Relative | R = (A + B)/ median(A + B) | First, calibrates for offset and allelic crosstalk. Second, performs quantile (self). | Post normalization, corrects for PCR fragment length and GC content. | - |
Affymetrix Power Tools (APT) | Relative | R = (A + B)/ median(A + B) | Quantile (self) | - | - |
CRLMM | Absolute | **Linear model | Quantile (HapMap) | - | Standard argument to specify in the linear model |