getPrintorder.Layout: Gets the order of the spots in which they were printed

In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description

Gets the order of the spots in which they were printed. The spots in column one were printed first, then the spots in column two and so on. By default the spot indices are returned.

Usage

## S3 method for class 'Layout'
getPrintorder(this, value=1:nbrOfSpots(this), ...)

Arguments

value

The elements to be placed in the resulting matrix.

Value

Returns a matrix with spot (values) printed at the same time in the same column. The first spots printed are in column one and the last ones printed in the last column. Often this means that there are nbrOfGrids(layout) rows and gridSize(layout) columns in the matrix. However, if the slide was printed in say two halfs (first half of the grids are printed and then the second), then this is not true.

Print order

The printing of a microarray is time consuming and often several microarray slides are printed at the same time, since it is even more time consuming to switch between the trays. When printing several microarrays at the same time, the arrayer prints the first spot in all grids on all slides, before moving on to the second spot. For a example, printing a batch of 100 slides with 6384 spots in 4x4 grids takes about 15 hours to print including manual work to switch trays etc. Each grid contains 19*21 spots, i.e. the arrayer has to put down the print tips 399 times on each slide, and in total 39900 times. This is about 44 put-downs a minute. It takes about 45-50 minutes to finish one row of spots.

Different directions

The most common print-order directions are "row-by-row" and "column-by-column". In both cases, when printing a slide at each print step nbrOfGrids(layout) spots are printed at the same time. The arrayer start of spotting the first spot in each of the grids. Then it cleans the print-tip heads, dries them, and go back to the trays to get a new set of cDNA and prints the second spot in each of the grids. The second spot is to the right to ("row-by-row") or below ("column-by-column") the first spot. When the array gets to the end of a row (column) it moves on to print the next row (column) and so on until all in all grids have been printed.

Print-order effects

An important factor for the quality of the printed spots is the temperature and the humidity. Too high temperature and humidity tends to produce too large spots that can even overlap [1]. If there is no automatic control for temperature and humidity, the quality of the spots could vary a lot between the spots printed during a 15 hours printing process. With a varying printing climate we should expect to see a variating of the quality of the spots along the order of which the spots are printed. The variation of temperature and humidity varies approximately in the time scale of hours. As it takes about 45-50 minutes to print a row of spots, we should therefore expect to see such a variation between the rows in the grids.

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

References

[1] Microarrays in Three Easy Steps, Priti Hedge, The Institute for Genomic Research, 200?.

See Also

For more information see Layout.

Examples

  layout <- Layout(2,2, 3,3)

  # No printorder specified - assumes de facto standard "row-by-row"
  print(getPrintorder(layout))

  #      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
  # [1,]    1    2    3    4    5    6    7    8    9
  # [2,]   10   11   12   13   14   15   16   17   18
  # [3,]   19   20   21   22   23   24   25   26   27
  # [4,]   28   29   30   31   32   33   34   35   36

  # Spots (1,10,19,28) were printed first, then (2,11,20,29), ...

  setPrintorder(layout, "column-by-column")
  print(getPrintorder(layout))

  #       [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
  # [1,]    1    4    7    2    5    8    3    6    9
  # [2,]   10   13   16   11   14   17   12   15   18
  # [3,]   19   22   25   20   23   26   21   24   27
  # [4,]   28   31   34   29   32   35   30   33   36

  # Spots (1,10,19,28) were printed first, then (4,13,22,31) below, ...

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.