[BioC] Quality Diagnostics of Affy Arrays using PLM

[Grant Izmirlian]

Just testing this out to see how replies work

On Monday, June 25, 2012 06:19:36 PM you 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.