printorder {limma} | R Documentation

## Identify Order in which Spots were Printed

### Description

Identify order in which spots were printed and the 384-well plate from which they were printed.

### Usage

    printorder(layout, ndups=1, spacing="columns", npins, start="topleft")

### Arguments

`layout` | list with the components `ngrid.r`, `ngrid.c`, `nspot.r` and `nspot.c`, or an `RGList` or `MAList` object from which the printer layout may be extracted.
`ndups` | number of duplicate spots, i.e., number of times print-head dips into each well
`spacing` | character string indicating layout of duplicate spots. Choices are `"columns"`, `"rows"` or `"topbottom"`.
`npins` | actual number of pins or tips on the print-head
`start` | character string giving position of the spot printed first in each grid. Choices are `"topleft"` or `"topright"` and partial matches are accepted.

### Details

In most cases the printer-head contains the `layout$ngrid.r` times `layout$ngrid.c` pins or tips and the array is printed using `layout$nspot.r` times `layout$npot.c` dips of the head. The plate holding the DNA to be printed is assumed to have 384 wells in 16 rows and 24 columns.

`ndups` indicates the number of spots printed from each well. The replicate spots from multiple dips into the same wells are assumed to be side-by-side by columns (`spacing="columns"`), by rows (`spacing="rows"`) or in the top and bottom halves of the array (`spacing="topbottom"`).

In some cases a smaller number of physical pins is used and the total number of grids is built up by effectively printing two or more sub-arrays on the same slide. In this case the number of grids should be a multiple of the number of pins.

Printing is assumed to proceed by rows within in each grid starting either from the top-left or the top-right.

### Value

List with components

`printorder` | numeric vector giving printorder of each spot, i.e., which dip of the print-head was used to print it
`plate` | numeric vector giving plate number from which each spot was printed
`plate.r` | numeric vector giving plate-row number of the well from which each spot was printed
`plate.c` | numeric vector giving plate-column number of the well from which each spot was printed
`plateposition` | character vector summarizing plate number and plate position of the well from which each spot was printed with letters for plate rows and number for columns. For example `02B13` is second row, 13th column, of the second plate.

### Author(s)

Gordon Smyth

### See Also

`normalizeForPrintorder`.

An overview of LIMMA functions for reading data is given in 03.ReadingData.

### Examples

    printorder(list(ngrid.r=2,ngrid.c=2,nspot.r=12,nspot.c=8))

[Package limma version 2.10.5 Index]