Description Usage Arguments Details Value Author(s) References See Also Examples

Compute the Z'-factor quality score.

1 |

`a, b` |
Matrices of control features. |

`method` |
a character vector, indicating which method should be
used to compute the Z'-factor. Default is |

The Z'-factor is a popular metric measuring the separation of control features in high-throughput screens. The original paper describing the Z'-factor is Zhang, 1999, J Biomol Screen.

Several univariate Z'-factor scores exist. The `original`

Z'-factor
from Zhang, 1999 is computed by Z' = 1 - 3*(sd(a)+sd(b))/abs(mean(a)-mean(b)).
A more rigorous definition of the score, implemented by the method `fixsd`

is given by Z' = 1 - 3*sqrt(var(a)+var(b))/abs(mean(a)-mean(b)), where the
pooled standard deviation is computed by the square root of the sum of the control
variances. A `robust`

method, less sensitive to outliers, is computed by
the relation Z' = 1-3*(mad(a)+mad(b))/abs(median(a)-median(b)) where the
control dispersions are computed with the mad and the control locations with the median.

A multivariate extension of the Z'-factor score can be designed by
linearly transforming the multivariate data to one dimension and
computing the standard (here, `fixsd`

) Z'-factor. It can be shown
that the linear transform that maximizes the score is the LDA. Moreover,
one can demonstrate that the resulting Z'-factor score is equivalent of
computing Z' = 1 - 3/dMaha(mu_a, mu_b, Sigma_a + Sigma_b) where
`dMaha`

is the Mahalanobis distance.

The Z'-factor, a numeric ranging from -infinity to 1.

Gregoire Pau, gregoire.pau@embl.de, 2010

J. H. Zhang, T. D. Chung, K. R. Oldenburg. A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays. J Biomol Screening, 1999.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
## initialize imageHTS object using the local submorph screen
local = tempdir()
server = system.file('submorph', package='imageHTS')
x = parseImageConf('conf/imageconf.txt', localPath=local, serverURL=server)
x = configure(x, 'conf/description.txt', 'conf/plateconf.txt', 'conf/screenlog.txt')
## get profiles
profiles = readHTS(x, type='file', filename='data/profiles.tab', format='tab')
a = profiles[match(getUnames(x, content='rluc'), profiles$uname),]
b = profiles[match(getUnames(x, content='ubc'), profiles$uname),]
## compute Z'-factor scores on some features
ft = c('med.c.t.m.majoraxis')
cat('Z\'-factor original=', zprime(a[,ft], b[,ft], 'original'), 'fixsd=', zprime(a[,ft], b[,ft], 'fixsd'), '\n')
## multivariate Z'-factor
ft = c('med.c.t.m.majoraxis', 'med.n.h.m.majoraxis', 'med.c.h.b.mean')
cat('Z\'-factor mahalanobis=', zprime(a[,ft], b[,ft], 'mahalanobis'), '\n')
``` |

imageHTS documentation built on Nov. 8, 2020, 8:29 p.m.

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