Question: arrayQualityMetrics::aqm.nuse and GeneST
8.9 years ago by
Tim Rayner • 270
Tim Rayner • 270 wrote:
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:  en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages:  tcltk stats graphics grDevices utils datasets methods  base other attached packages:  Rmpi_0.5-8 affyPara_1.10.0  aplpack_1.2.3 snow_0.3-3  hugene10stv1cdf_3.24.1 arrayQualityMetrics_3.2.0  affyPLM_1.26.0 preprocessCore_1.12.0  gcrma_2.22.0 affy_1.28.0  vsn_3.18.0 Biobase_2.10.0 loaded via a namespace (and not attached):  affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0  beadarray_2.0.1 Biostrings_2.18.0 DBI_0.2-5  genefilter_1.32.0 grid_2.12.0 hwriter_1.2  IRanges_1.8.2 lattice_0.19-13 latticeExtra_0.6-14  limma_3.6.6 marray_1.28.0 RColorBrewer_1.0-2  RSQLite_0.9-3 simpleaffy_2.26.0 splines_2.12.0  stats4_2.12.0 survival_2.36-1 SVGAnnotation_0.6-0  tools_2.12.0 XML_3.2-0 xtable_1.5-6 -- Tim Rayner Bioinformatician, Smith Lab CIMR, University of Cambridge, U.K.
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