[BioC] arrayQualityMetrics problem with Agilent 2-colour

Edwin Groot edwin.groot at biologie.uni-freiburg.de
Wed Jun 23 12:22:16 CEST 2010

Hello all,
Would anyone know of a simple way to plot the heatmap in
arrayQualityMetrics on a per-channel basis, rather than the per-array

I have 16 2-colour Agilent arrays read in by the LIMMA package, but
arrayQualityMetrics shows only 16 arrays in the heatmap, rather than
the 32 red and green samples that I would expect. When one array is an
outlier in the heatmap, I do not know which sample (red or green) is at

The code that I used is quite simple:
> library(limma)
> library(arrayQualityMetrics)
> targets <- readTargets("qc.exp")
> RG <- read.maimages(targets$FileName, source="agilent")
> arrayQualityMetrics(expressionset=RG, outdir="default", force = TRUE,
do.logtransform = TRUE)
The directory 'default' has been created.
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
(loaded the KernSmooth namespace)

I also attempted a custom call to aqm.* functions. However, the
preparatory step fails:
> RGprep = aqm.prepdata(expressionset=RG, do.logtransform = TRUE)
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "aqm.prepdata", for
signature "RGList"

> sessionInfo()
R version 2.11.1 (2010-05-31) 

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] arrayQualityMetrics_2.6.0 affyPLM_1.24.0           
[3] preprocessCore_1.10.0     gcrma_2.20.0             
[5] affy_1.26.1               Biobase_2.8.0            
[7] limma_3.4.2              

loaded via a namespace (and not attached):
 [1] affyio_1.16.0        annotate_1.26.0      AnnotationDbi_1.10.1
 [4] beadarray_1.16.0     Biostrings_2.16.3    DBI_0.2-5           
 [7] genefilter_1.30.0    grid_2.11.1          hwriter_1.2         
[10] IRanges_1.6.4        lattice_0.18-8       latticeExtra_0.6-11 
[13] marray_1.26.0        RColorBrewer_1.0-2   RSQLite_0.9-1       
[16] simpleaffy_2.24.0    splines_2.11.1       stats4_2.11.1       
[19] survival_2.35-8      tools_2.11.1         vsn_3.16.0          
[22] xtable_1.5-6        

Thanks in advance,
Dr. Edwin Groot, postdoctoral associate
AG Laux
Institut fuer Biologie III
Schaenzlestr. 1
79104 Freiburg, Deutschland
+49 761-2032945

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