dyebias.umcu.proper.estimators {dyebiasexamples}R Documentation

Determine which spots should not be ruled out as slide bias estimators

Description

Some spots (reporters/probes) should not be used when estimating the slide bias. Typical examples are mitochondrial genes and spots known to cross-hybridize. This function finds the ones that are OK to use.

Arguments

reporter.info A data.frame, one row per spot, with (at least) columns reporterId (e.g. gene id or oligo id) and any of the following characteristics: reporterGroup, chromosomeName, bioSeqType, crosshybRank and reporterSequence. They are used to get rid of reporters that are not suitable when estimating the slide bias.
verbose Logical speficying whether to be verbose or not

Details

This function is particular to the slides and database set-up at the Holstege lab, but might serve as inspiration.

Value

Returns and index vector that can be used as the estimator.subset-argument to dyebias.application.subset.

Author(s)

Philip Lijnzaad p.lijnzaad@umcutrecht.nl

References

Margaritis, T., Lijnzaad, P., van~Leenen, D., Bouwmeester, D., Kemmeren, P., van~Hooff, S.R and Holstege, F.C.P. (2009) Adaptable gene-specific dye bias correction for two-channel DNA microarrays. Molecular Systems Biology, submitted

See Also

dyebias.apply.correction

Examples


  

  ### choose the estimators and which spots to correct:
  estimator.subset <- dyebias.umcu.proper.estimators(maInfo(maGnames(data.norm)))

  summary(estimator.subset)

  ### do the correction
  ## Not run: 
     correction <- dyebias.apply.correction(data.norm=data.norm,
                                         iGSDBs = iGSDBs.estimated,
                                         estimator.subset=estimator.subset,
                                         application.subset = TRUE,
                                         verbose=TRUE)
   
## End(Not run)
[Package dyebiasexamples version 1.0.3 Index]