[BioC] Quality Diagnostics of Affy Arrays using PLM

[Grant Izmirlian [guest]]

Hi:  
I have been following examples listed in section 3.5.1 of "Bioinformatics and Computational Biology using R and Bioconductor", which deals with quality diagnostics of affy arrays using PLM.  I am trying to produce a composite plot displaying per chip residuals from the PLM model using my own data.  Following the example, starting with the AffyBatch object, MyDat.AffyBatch, which contains 40 arrays,

MyDat.plm <- fitPLM(MyDat.AffyBatch)
par(mfrow=c(4,10))
image(MyDat.plm, type="resids", which=1)
image(MyDat.plm, type="resids", which=2)
image(MyDat.plm, type="resids", which=3)
.
.
.
image(MyDat.plm, type="resids", which=40)

The problem is that the par(mfrow=c(4,10)) is ignored and I get 
40 new plots.  I tried setting 'add=TRUE' to the argument list above--still no luck.

The example in the text makes it appear that this works.  What's going on?





 -- output of sessionInfo(): 

R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 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] hgu133plus2cdf_2.9.1  AnnotationDbi_1.16.10 limma_3.10.0         
[4] affyPLM_1.30.0        preprocessCore_1.16.0 gcrma_2.26.0         
[7] affy_1.32.0           Biobase_2.14.0       

loaded via a namespace (and not attached):
 [1] affyio_1.22.0       BiocInstaller_1.2.1 Biostrings_2.22.0  
 [4] DBI_0.2-5           IRanges_1.12.5      RSQLite_0.11.1     
 [7] splines_2.14.0      tcltk_2.14.0        tools_2.14.0       
[10] zlibbioc_1.0.0     


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