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


A denotes the A-allele intensity and B the B-allele intensity for the corresponding probe.

* Rexp is computed from linear interpolation of canonical genotype clusters [4].

** Corrects for optical noise and non-specific binding in the linear model.

Eckel-Passow et al. BMC Bioinformatics 2011 12:220   doi:10.1186/1471-2105-12-220

Open Data