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Last seen 10.3 years ago
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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