Hi, I think I've run into a bug on the latest arrayQualityMetrics release. I'm running the function on an AffyBatch object created from HuGene ST 1.0 CEL files which I've tested with previous versions of arrayQualityMetrics without any problems: > arrayQualityMetrics(cd8, outdir='canonical_qc') The directory 'canonical_qc' has been created. Error in quantile.default(dataprep$dat[ss, ], probs = 0.01) : missing values and NaN's not allowed if 'na.rm' is FALSE Error in density.default(as.matrix(log2(mm(expressionset))), ...) : 'x' contains missing values In addition: Warning message: In nuse$legend = paste(phrase$fig("Normalized Unscaled Standard Error (NUSE)"), : Coercing LHS to a list It appears that the aqm.nuse() function is throwing the error. The error does not occur if I use CELs from the HG-U133A platform, so I'm guessing that it's a problem running the function on CELs from the PM-only Gene ST platform? Aside from that, thank you very much for the improvements with this release; the new QC plots very useful indeed. Best regards, Tim Rayner sessionInfo() follows: R version 2.12.0 (2010-10-15) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Rmpi_0.5-8 affyPara_1.10.0 [3] aplpack_1.2.3 snow_0.3-3 [5] hugene10stv1cdf_3.24.1 arrayQualityMetrics_3.2.0 [7] affyPLM_1.26.0 preprocessCore_1.12.0 [9] gcrma_2.22.0 affy_1.28.0 [11] vsn_3.18.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 [4] beadarray_2.0.1 Biostrings_2.18.0 DBI_0.2-5 [7] genefilter_1.32.0 grid_2.12.0 hwriter_1.2 [10] IRanges_1.8.2 lattice_0.19-13 latticeExtra_0.6-14 [13] limma_3.6.6 marray_1.28.0 RColorBrewer_1.0-2 [16] RSQLite_0.9-3 simpleaffy_2.26.0 splines_2.12.0 [19] stats4_2.12.0 survival_2.36-1 SVGAnnotation_0.6-0 [22] tools_2.12.0 XML_3.2-0 xtable_1.5-6 -- Tim Rayner Bioinformatician, Smith Lab CIMR, University of Cambridge, U.K.

Hi Tim, this is the result of (perhaps overzealous) tightening of the code that I did in the meanwhile. In previous versions, when the computations for a certain module (i.e. a figure) of the report failed, the 'arrayQualityMetrics' function would just silently catch the exception and continue with the other modules. Now, the error leads to the function being stopped and the error becoming visible to the user. I thought that this is more transparent, but it will need further refinement to provide an informative error message and concrete suggestions of what to do for trouble-shooting. I am looking forward to users' feedback here. In the release version 3.2.0, sadly, not all the consequences of this big refactoring exercise have been well enough tested (my fault). 1. To that end, can you make the offending object 'cd8' available to me for testing (e.g. via dropbox)? 2. For you to be able to use the package, I propose a two-step solution: On the short term, copy the function 'arrayQualityMetrics' out of the package, and make the part that is headed "##--Affymetrix specific modules--" optional (e.g. by making it depend on a user-definable logical switch). I will do the same with the devel version, and within 1-2 months, that version should again be ready for production use. Best wishes Wolfgang Tim Rayner scripsit 10/11/10 12:52: > Hi, > > I think I've run into a bug on the latest arrayQualityMetrics release. > I'm running the function on an AffyBatch object created from HuGene ST > 1.0 CEL files which I've tested with previous versions of > arrayQualityMetrics without any problems: > >> arrayQualityMetrics(cd8, outdir='canonical_qc') > The directory 'canonical_qc' has been created. > Error in quantile.default(dataprep$dat[ss, ], probs = 0.01) : > missing values and NaN's not allowed if 'na.rm' is FALSE > Error in density.default(as.matrix(log2(mm(expressionset))), ...) : > 'x' contains missing values > In addition: Warning message: > In nuse$legend = paste(phrase$fig("Normalized Unscaled Standard Error > (NUSE)"), : > Coercing LHS to a list > > It appears that the aqm.nuse() function is throwing the error. The > error does not occur if I use CELs from the HG-U133A platform, so I'm > guessing that it's a problem running the function on CELs from the > PM-only Gene ST platform? > > Aside from that, thank you very much for the improvements with this > release; the new QC plots very useful indeed. > > Best regards, > > Tim Rayner > > > > sessionInfo() follows: > > R version 2.12.0 (2010-10-15) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] tcltk stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Rmpi_0.5-8 affyPara_1.10.0 > [3] aplpack_1.2.3 snow_0.3-3 > [5] hugene10stv1cdf_3.24.1 arrayQualityMetrics_3.2.0 > [7] affyPLM_1.26.0 preprocessCore_1.12.0 > [9] gcrma_2.22.0 affy_1.28.0 > [11] vsn_3.18.0 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0 > [4] beadarray_2.0.1 Biostrings_2.18.0 DBI_0.2-5 > [7] genefilter_1.32.0 grid_2.12.0 hwriter_1.2 > [10] IRanges_1.8.2 lattice_0.19-13 latticeExtra_0.6-14 > [13] limma_3.6.6 marray_1.28.0 RColorBrewer_1.0-2 > [16] RSQLite_0.9-3 simpleaffy_2.26.0 splines_2.12.0 > [19] stats4_2.12.0 survival_2.36-1 SVGAnnotation_0.6-0 > [22] tools_2.12.0 XML_3.2-0 xtable_1.5-6 > > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber