median of the NUSE value
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@kfbargadehues-1528
Last seen 10.3 years ago
Dear list, I am using affyPLM for my QC, and am trying to obtain the median of the NUSE values for my chips. if I type >NUSE(Pset, main = "NUSE values") I get the NUSE boxplot but if I type > NUSE(Pset, type = "stats") Error in match.arg(type) : 'arg' should be one of plot, values or > NUSE(Pset, type = "values") Error in x at weights[which, ] : incorrect number of dimensions In addition: Warning messages: 1: longer object length is not a multiple of shorter object length in: model == (PM ~ - 1 + probes + samples) 2: longer object length is not a multiple of shorter object length in: model == (PM ~ - 1 + samples + probes) 3: the condition has length > 1 and only the first element will be used in: if ((model == (PM ~ -1 + probes + samples)) | (model == (PM ~ my sessionInfo() Version 2.3.0 (2006-04-24) i386-pc-mingw32 attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "tools" "methods" "base" other attached packages: hgu133plus2cdf affyPLM gcrma matchprobes affydata affy affyio Biobase "1.12.0" "1.8.0" Any suggestions?? Also, is it possible to colour the boxes of the boxplot? I have so far been using boxplot() for Pset with the argument "col", but it does not work for NUSE() Thanks in advance, David
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio • 1.3k views
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Ben Bolstad ★ 1.2k
@ben-bolstad-1494
Last seen 7.3 years ago
Below is my results using affyPLM 1.9.5. No particular problem here with that version. What was your fitPLM call? > Pset <- fitPLM(Dilution) Background correcting PM Normalizing PM Fitting models > NUSE(Pset,main="NUSE values",col=rainbow(4)) > NUSE(Pset,type="stats") 20A 20B 10A 10B median 0.99929158 0.99939860 1.00213287 0.99927522 IQR 0.02592881 0.02963567 0.02816327 0.02591606 > NUSE(Pset,type="stats") 20A 20B 10A 10B median 0.99929158 0.99939860 1.00213287 0.99927522 IQR 0.02592881 0.02963567 0.02816327 0.02591606 On Thu, 2006-06-15 at 13:11 +0200, kfbargad at ehu.es wrote: > Dear list, > > I am using affyPLM for my QC, and am trying to obtain the median of > the NUSE values for my chips. > > if I type > >NUSE(Pset, main = "NUSE values") > I get the NUSE boxplot > > but if I type > > NUSE(Pset, type = "stats") > Error in match.arg(type) : 'arg' should be one of plot, values > or > > NUSE(Pset, type = "values") > Error in x at weights[which, ] : incorrect number of dimensions > In addition: Warning messages: > 1: longer object length > is not a multiple of shorter object length in: model == (PM ~ - > 1 + probes + samples) > 2: longer object length > is not a multiple of shorter object length in: model == (PM ~ - > 1 + samples + probes) > 3: the condition has length > 1 and only the first element will be > used in: if ((model == (PM ~ -1 + probes + samples)) | (model == (PM ~ > > my sessionInfo() > Version 2.3.0 (2006-04-24) > i386-pc-mingw32 > > attached base packages: > [1] "stats" "graphics" "grDevices" "utils" "datasets" "tools" > "methods" "base" > > other attached packages: > hgu133plus2cdf affyPLM gcrma matchprobes > affydata affy affyio Biobase > "1.12.0" "1.8.0" > > > Any suggestions?? > > Also, is it possible to colour the boxes of the boxplot? I have so far > been using > boxplot() for Pset with the argument "col", but it does not work for > NUSE() > > > Thanks in advance, > > David > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Ben Bolstad <bmb at="" bmbolstad.com=""> http://bmbolstad.com
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Dear Ben and list, I have just rerun my code and now it works fine. Sorry for bothering, there was probably some typo. Regards, David > Below is my results using affyPLM 1.9.5. No particular problem here > with that version. What was your fitPLM call? > > > > > > > > > Pset <- fitPLM(Dilution) > Background correcting PM > Normalizing PM > Fitting models > > NUSE(Pset,main="NUSE values",col=rainbow(4)) > > NUSE(Pset,type="stats") > 20A 20B 10A 10B > median 0.99929158 0.99939860 1.00213287 0.99927522 > IQR 0.02592881 0.02963567 0.02816327 0.02591606 > > NUSE(Pset,type="stats") > 20A 20B 10A 10B > median 0.99929158 0.99939860 1.00213287 0.99927522 > IQR 0.02592881 0.02963567 0.02816327 0.02591606 > > On Thu, 2006-06-15 at 13:11 +0200, kfbargad at ehu.es wrote: > > Dear list, > > > > I am using affyPLM for my QC, and am trying to obtain the median of > > the NUSE values for my chips. > > > > if I type > > >NUSE(Pset, main = "NUSE values") > > I get the NUSE boxplot > > > > but if I type > > > NUSE(Pset, type = "stats") > > Error in match.arg(type) : 'arg' should be one of plot, values > > or > > > NUSE(Pset, type = "values") > > Error in x at weights[which, ] : incorrect number of dimensions > > In addition: Warning messages: > > 1: longer object length > > is not a multiple of shorter object length in: model == (PM ~ - > > 1 + probes + samples) > > 2: longer object length > > is not a multiple of shorter object length in: model == (PM ~ - > > 1 + samples + probes) > > 3: the condition has length > 1 and only the first element will be > > used in: if ((model == (PM ~ -1 + probes + samples)) | (model == (PM ~ > > > > my sessionInfo() > > Version 2.3.0 (2006-04-24) > > i386-pc-mingw32 > > > > attached base packages: > > [1] "stats" "graphics" "grDevices" "utils" "datasets" "tools" > > "methods" "base" > > > > other attached packages: > > hgu133plus2cdf affyPLM gcrma matchprobes > > affydata affy affyio Biobase > > "1.12.0" "1.8.0" > > > > > > Any suggestions?? > > > > Also, is it possible to colour the boxes of the boxplot? I have so far > > been using > > boxplot() for Pset with the argument "col", but it does not work for > > NUSE() > > > > > > Thanks in advance, > > > > David > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- > Ben Bolstad <bmb at="" bmbolstad.com=""> > http://bmbolstad.com > >
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