maCompPlate2 {stepNorm} | R Documentation |

This function is a modification of the `maCompPlate`

function in the `marrayClasses`

library. It generates plate IDs
from the dimensions of the grid and spot matrices. Unlike the
`maCompPlate`

function, the number of spots is not
necessarily a multiple of the number of wells on a plate, therefore
this function allows empty spots on the slide.

maCompPlate2(no.plates = NULL, n = 384)

`no.plates` |
object of class "numeric", number of plates used specified by the user. If a number is not specified, then it is assumed that there are no empty spots on the slide. |

`n` |
object of class "numeric", number of wells in each plate, usually 384 or 96. |

This function can be used to handle three cases: 1) the number of spots is a multiple of the number of wells on a plate (usually 96 or 384); 2) the number of spots is not a multiple of the number of wells on a plate, and several of spots on the slide are therefore left empty. In this case, the user needs to specify the number of total plates used; plate IDs of empty spots will be NAs; 3)the number of spots is not a multiple of the number of wells on a plate, but all spots on the slide are spotted, therefore there is one plate not fully used. In this case, the user does not need to specify the number of total plates (as this will not be an integer), the function assumes no empty spots on the slide automatically. See Examples below.

The function `maCompPlate2`

returns a function with bindings for
`no.plates`

and `n`

, which when receiving a object of
`marrayRaw`

,
`marrayNorm`

or `marrayLayout`

class, it returns a
vector of plate IDs (`factor`

).

Yuanyuan Xiao

####### case 1: no empty spots on the slide, full plates used L<-new("marrayLayout", maNgr=4, maNgc=4, maNsr=22, maNsc=24) ### "compPlate" is a function compPlate <- maCompPlate2(n=384) plate <- compPlate(L) table(plate) ### can also use: plate<-maCompPlate(L,384) table(plate) ####### case 2: with empty spots on the slide, full plates used L<-new("marrayLayout", maNgr=4, maNgc=4, maNsr=22, maNsc=26) ### "compPlate" is a function compPlate <- maCompPlate2(no.plates=22,n=384) plate <- compPlate(L) table(plate) ### empty spots are NAs unique(plate) ###### case 3: no empty spots on the slide, one plate not full L<-new("marrayLayout", maNgr=4, maNgc=4, maNsr=22, maNsc=26) ### argument no.plates not specified, the function assumes no empty spots compPlate <- maCompPlate2(n=384) plate <- compPlate(L) ### 23 full plates (384), the 24th not full (304) table(plate) ### no NAs, no empty spots unique(plate)

[Package *stepNorm* version 1.0.2 Index]