[BioC] Problems with arrayQualityMetrics

[Audrey Kauffmann]

Dear Ingunn,

Can you please show the content of the column "experiment"? Apparently
this is the cause of the failure.
Also, if you are just interested in re-running the PCA with the
colouring accordingly to "experiment" instead of "pRed", you can just
use the function aqm.predata() and subsequently aqm.pca().

Best wishes,
Audrey

2010/7/1 Ingunn Berget <ingunn.berget at umb.no>:
> Dear List
>
> I have a cDNA microarray data set with 33696 probes and 36 arrays
> Variables defined in RG$target are
>
> names(RG$targets)
> [1] "ShortName"  "pRed"       "pGreen"     "IDRed"      "IDGreen"
> [6] "cdiff"      "experiment"
>
> "pRed" indicates what type of samples that are labelled with the red dye (two different types of samples)
> "experiment" indicates in which experiment (1 or 2) the array was run.
>
> I have used arrayQualityMetrics for quality control.
>
> The command I have run before is this
>
> arrayQualityMetrics(RG,outdir = mydir, do.logtransform = TRUE,grouprep = TRUE, intgroup = c("pRed","experiment"), force = TRUE)
>
> this worked fine
>
> I know want to redo the analysis, but with intgroup = c("experiment","pRed") instead to get different colouring in pca plot and heatmap diagram
>
> So I tried this command:
> arrayQualityMetrics(RG,outdir = mydir, do.logtransform = TRUE,grouprep = TRUE, intgroup = c("experiment","pRed"), force = TRUE)
>
> and the computer was running and running ...
>
> then I tried
>
> arrayQualityMetrics(RG,outdir = mydir, do.logtransform = TRUE,grouprep = TRUE, intgroup = c("experiment","pRed"), force = TRUE,spatial = FALSE)
>
> and the computer was running and running ...
>
> I let this go for approximately half a day and one night and then stopped it.
> I don't really know how much time this took the first time I ran the command, but I am sure that I did not wait for a very long time.
> Moreover it is only the heatmap, pca plots and box plots that will be different so how can I generate these without doing the complete analysis?
>
> Ingunn
>
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> i686-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] splines   grid      stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] MASS_7.3-5                convert_1.24.0
>  [3] marray_1.26.0             ggplot2_0.8.7
>  [5] digest_0.4.2              reshape_0.8.3
>  [7] plyr_0.1.9                proto_0.3-8
>  [9] arrayQualityMetrics_2.6.0 affyPLM_1.24.0
> [11] preprocessCore_1.10.0     gcrma_2.20.0
> [13] affy_1.26.1               Biobase_2.8.0
> [15] limma_3.4.3
>
> 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_2.16.5    DBI_0.2-5
>  [7] genefilter_1.30.0    hwriter_1.2          IRanges_1.6.6
> [10] lattice_0.18-5       latticeExtra_0.6-11  RColorBrewer_1.0-2
> [13] RSQLite_0.9-1        simpleaffy_2.24.0    stats4_2.11.0
> [16] survival_2.35-8      tools_2.11.0         vsn_3.16.0
> [19] xtable_1.5-6
>>
>
>
>
> Ingunn Berget (Dr. Scient)
> UMB, box 5003, IHA
> 1432 Ås
> Norway
>
> Centre for Integrative Genetics, www.cigene.no
> Centre for Biospectroscopy and Data Modelling, www.specmod.org
>
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>



-- 
Audrey Kauffmann
Bergonie Cancer Institute
229 Cours de l'Argonne
33076 Bordeaux
France