Description Usage Arguments Value Examples

`create_assay`

makes a new object of class assay. You should pass this object to `detect_bias()`

and `correct_bias()`

methods

1 | ```
create_assay(m, ctrl = NA)
``` |

`m` |
The assay you want to be corrected |

`ctrl` |
An optional boolean array of the same dimensions as |

assay The created assay object. It containts the following fields:

`n`

The HTS matrix of raw measurements

`ctrl`

The binary matrix of control wells

`biasPositions`

The binary matrix where 1:well is biased, 0:well is unbiased, as suggested by Mann-Whitney test

`mCorrected`

The HTS matrix of corrected measurements, initilized to a zero array, and subsequently storing the corrected version of `m`

via `correct_bias()`

`biasType`

Vector of length p, where p is the number of plates. It tells, for each plate of the assay, A:Additive trend, M:Multiplicative trend, U:Undetermined trend and C:Error-free plate.

`biasModel`

Vector of length p, where p is the number of plates. It tells, for each plate of the assay, the most likely spatial bias model (1 through 6)

`biasConf`

Vector of length p, where p is the number of plates. It tells, for each plate of the assay, the confidence in the model, (0 - lowest to 3- highest). It is computed by counting the number of bias models (additive or mutliplicative) which agree together.

1 2 3 4 | ```
# Fictive 8x12x5 assay
assay<-create_assay(m)
# Plate 7 taken from Carralot et al. 2012
assay<-create_assay(plate7)
``` |

```
Loading required package: RColorBrewer
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: kSamples
Loading required package: SuppDists
Loading required package: RVAideMemoire
*** Package RVAideMemoire v 0.9-73 ***
```

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.