toPrintorderMatrix.Layout: Gets a matrix of spot indices in the order they were printed
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Details Value Author(s) References See Also Examples

Gets a matrix of spot indices in the order 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.

1 2	## S3 method for class 'Layout' toPrintorderMatrix(this, value=seq(nbrOfSpots(this)), ...)

value

The elements to be placed in the resulting matrix.

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. The 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 of the first spot. When the array gets to the end of a row it has printed the first line of each grid. The arrayer now moves on to print the spots in line two, three and so on until all lines in all grids have been printed.

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.

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.

Returns a matrix with nbrOfGrids(layout) rows and gridSize(layout) columns.

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

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

For more information see Layout.

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

  print(toPrintorderMatrix(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

  # Spot 1, 10, 19 and 28 were printed first, then 2, 11, 20, and 29...