[BioC] Plate or print-order effects - limma

[Gordon Smyth]

At 07:38 AM 3/01/2007, Jenny Drnevich wrote:
>Hi Gordon,
>
>FYI - I was playing around with plotting print order effects, and 
>found a discrepancy between the help documentation and the actual 
>behavior of 'normalizeForPrintorder.rg '. The help file states "The 
>function plotPrintorder or normalizeForPrintorder.rg with plot=TRUE 
>returns no value but produces a plot as a side-effect." However, 
>when I used 'normalizeForPrintorder.rg' with plot=TRUE, it not only 
>produced the plot but spit out the entire list!

You're right. I'll fix.

>I'm using this function instead of the wrapper 'plotPrintorder' 
>because I'm having trouble making the necessary layout list. I could 
>only find a little bit of information about the layout list in 
>'printorder' help page - is each component of the list (ngrid.r, 
>ngrid.c, nspot.r and nspot.c) just a single number? In my case our 
>printer has 48 tips and prints 12 x 4 blocks of 420 spots, one dip 
>per spot, so would my layout just be a list of ngrid.r = 12, ngrid.c 
>= 4, nspot.r = 420, and nspot.c = 1?

You also need to know the number of rows (nspot.r) and columns 
(nspot.c) of spots in each block. nspot.c is almost certainly greater than 1.

You also need to check with your microarray printing unit whether 
printing of your arrays begins in the top right or top left of each 
block, and whether it proceeds by rows or columns. The default for 
normalizeForPrintorder assumes topleft by rows, which the usual setup 
at UCSF. But the AGRF in Australia uses topright by rows.

See help("PrinterLayout-class"). The read.maimages() function 
produces the printer layout information automatically as RG$printer 
for some input sources including GenePix and ImageGene.

Best wishes
Gordon

>Thanks,
>Jenny
>
> > sessionInfo()
>R version 2.4.0 (2006-10-03)
>i386-pc-mingw32
>
>locale:
>LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
>States.1252;LC_MONETARY=English_United 
>States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
>attached base packages:
>[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
>[7] "utils"     "datasets"  "base"
>
>other attached packages:
>  affyQCReport    simpleaffy         made4 scatterplot3d          ade4
>      "1.12.0"       "2.8.0"       "1.8.0"      "0.3-24"       "1.4-2"
>       affyPLM      affydata affycoretools       annaffy        xtable
>      "1.10.0"      "1.10.0"       "1.7.5"       "1.6.0"       "1.4-2"
>         gcrma   matchprobes       biomaRt         RCurl           XML
>       "2.6.0"       "1.6.0"       "1.8.0"       "0.7-0"       "1.2-0"
>       GOstats      Category    genefilter      survival          KEGG
>       "2.0.3"       "2.0.3"      "1.12.0"        "2.29"      "1.14.1"
>          RBGL      annotate            GO         graph         limma
>      "1.10.0"      "1.12.0"      "1.14.1"      "1.12.0"       "2.9.1"
>          affy        affyio       Biobase       RWinEdt
>      "1.12.1"       "1.2.0"      "1.12.2"       "1.7-5"
>
>Jenny Drnevich, Ph.D.
>
>Functional Genomics Bioinformatics Specialist
>W.M. Keck Center for Comparative and Functional Genomics
>Roy J. Carver Biotechnology Center
>University of Illinois, Urbana-Champaign
>
>330 ERML
>1201 W. Gregory Dr.
>Urbana, IL 61801
>USA
>
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich at uiuc.edu