[BioC] MAplot form arrayQualityMetrics

[Ingunn Berget]

Dear List

I have run arrayQualityMetrics with an RG list as input to look at the quality diagnostics for a set of cDNA arrays.
There are 28 arrays, but there are only 8 MAplots in the maplot.pdf/maplot.png files. 
In the other plots I get results for all other arrays (28 boxes in boxplots, 28 subplots in spatial plots and so on).


The command to run the arrayQualitMatrics function: 

aqm.res <- arrayQualityMetrics(expressionset = RG,outdir = "AQM",
  force=TRUE, intgroup = "Cy3",grouprep = TRUE,do.logtransform = TRUE)


I also get a lot of warnings:


Warning messages:
1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
2: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
3: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
4: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
5: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
6: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'


I hope that someone can give me some hints of why I don't see MAplot for all arrays, and a solution to the warnings


> sessionInfo()
R version 2.9.2 (2009-08-24) 
i386-pc-mingw32 

locale:
LC_COLLATE=Norwegian (Bokmål)_Norway.1252;LC_CTYPE=Norwegian (Bokmål)_Norway.1252;LC_MONETARY=Norwegian (Bokmål)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokmål)_Norway.1252

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

other attached packages:
 [1] arrayQualityMetrics_2.2.2 affyPLM_1.20.0            preprocessCore_1.6.0      gcrma_2.16.0             
 [5] Biostrings_2.12.8         IRanges_1.2.3             affy_1.22.1               Biobase_2.4.1            
 [9] plyr_0.1.9                limma_2.18.2              svSocket_0.9-43           svMisc_0.9-48            
[13] TinnR_1.0.3               R2HTML_1.59-1             Hmisc_3.6-1              

loaded via a namespace (and not attached):
 [1] affyio_1.12.0       annotate_1.22.0     AnnotationDbi_1.6.1 beadarray_1.12.0    cluster_1.12.0     
 [6] DBI_0.2-4           genefilter_1.24.2   grid_2.9.2          hwriter_1.1         KernSmooth_2.23-2  
[11] lattice_0.17-25     latticeExtra_0.6-1  marray_1.22.0       RColorBrewer_1.0-2  RSQLite_0.7-2      
[16] simpleaffy_2.20.0   splines_2.9.2       stats4_2.9.2        survival_2.35-4     tools_2.9.2        
[21] vsn_3.12.0          xtable_1.5-5       
> 

Best regards
Ingunn