[BioC] arrayQualityMetrics problem with Agilent 2-colour

[Audrey Kauffmann]

Hi Edwin,

arrayQualityMetrics is not really appropriate for that, maybe you can
consider using the clustering and heatmap functions outside from the
package.

Also, regarding using aqm.prepdata on a RGList is not implemented, you
would first need to convert your RGList into a NChannelSet.

A trick, not recommended but which would work, is to convert your
RGList as an ExpressionSet (usually for one channel) where each R and
G channels would be treated as separated chips, then use aqm.prepdata
and aqm.heatmap.

Please let me know if you have more questions regarding this,
Audrey

2010/6/23 Edwin Groot <edwin.groot at biologie.uni-freiburg.de>:
> 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
> basis?
>
> 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
> fault.
>
> 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)
> [[1]]
> [[2]]
>
> 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)
> i486-pc-linux-gnu
>
> locale:
>  [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
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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,
> Edwin
> --
> Dr. Edwin Groot, postdoctoral associate
> AG Laux
> Institut fuer Biologie III
> Schaenzlestr. 1
> 79104 Freiburg, Deutschland
> +49 761-2032945
>
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-- 
Audrey Kauffmann
Bergonie Cancer Institute
229 Cours de l'Argonne
33076 Bordeaux
France
+33.5.56.33.04.53