zprime: Compute the Z'-factor quality score
In imageHTS: Analysis of high-throughput microscopy-based screens

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

Compute the Z'-factor quality score.

1	zprime(a, b, method=c('mahalanobis', 'robust', 'fixsd', 'original'))

`a, b`	Matrices of control features.
`method`	a character vector, indicating which method should be used to compute the Z'-factor. Default is `mahalanobis`. See Details.

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.

readHTS

  ## 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')