[BioC] Plate or print-order effects - limma

[Jenny Drnevich]

Hi Gordon,

Thanks for your help. Here's one correction for the archives and a small 
suggestion:

>See help("PrinterLayout-class").

this should be help("PrintLayout-class")


>The read.maimages() function produces the printer layout information 
>automatically as RG$printer for some input sources including GenePix and 
>ImageGene.

The PrintLayout class help page does explain everything pretty well, and I 
was happy to see that I already had RG$printer because I had GenePix data. 
I would suggest a small change to the help page of Print-Order 
Normalization, that the argument 'layout' wants an object of class 
'PrintLayout' (or a similar list). That would have helped me make the 
connection and find the information.

Thanks,
Jenny



>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

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