Question: Quality Diagnostics of Affy Arrays using PLM
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Guest User12k 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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ADD COMMENTlink modified 7.0 years ago by Ben Bolstad1.2k • written 7.0 years ago by Guest User12k
Answer: Quality Diagnostics of Affy Arrays using PLM
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gravatar for Grant Izmirlian
7.0 years ago by
Grant Izmirlian10 wrote:
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.
ADD COMMENTlink written 7.0 years ago by Grant Izmirlian10
Answer: Quality Diagnostics of Affy Arrays using PLM
0
gravatar for Ben Bolstad
7.0 years ago by
Ben Bolstad1.2k
Ben Bolstad1.2k wrote:
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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.0 years ago by Ben Bolstad1.2k
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