[BioC] Quality Diagnostics of Affy Arrays using PLM

[Benjamin Bolstad]

Hi Grant,

I can not reproduce this issue at my end. But my suspicion is that when you put the "add=TRUE" argument into your image() on the PLMset it is expanding this to "add.legend=TRUE".  Internally the image() method for the PLMset object uses "layout" in this situation (which will not interact very well with "par(mfrow)"


Best,

Ben

On Jun 25, 2012, at 3:19 PM, Grant Izmirlian [guest] wrote:

> 
> 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     
> 
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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