Question: Quality Diagnostics of Affy Arrays using PLM
6.8 years ago by
Guest User • 12k
Guest User • 12k 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:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  hgu133plus2cdf_2.9.1 AnnotationDbi_1.16.10 limma_3.10.0  affyPLM_1.30.0 preprocessCore_1.16.0 gcrma_2.26.0  affy_1.32.0 Biobase_2.14.0 loaded via a namespace (and not attached):  affyio_1.22.0 BiocInstaller_1.2.1 Biostrings_2.22.0  DBI_0.2-5 IRanges_1.12.5 RSQLite_0.11.1  splines_2.14.0 tcltk_2.14.0 tools_2.14.0  zlibbioc_1.0.0 -- Sent via the guest posting facility at bioconductor.org.
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