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]