[BioC] Problems with arrayQualityMetrics

[Ingunn Berget]

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