Dear all,
recently I am encountering problems using arrayQualityMetrics. Execution is always stopped at the same point and an error is thrown:
"Error in file.info(x): invalid filename argument"
Figure 1 (Distances between arrays) and Figure 2 (Outlier detection for Distances between arrays) are always created successfully, but nothing more. This happens to me on Ubuntu as well as on OS X.
I tried with different data sets, but nothing worked. I'm calling arrayQualityMetrics() with:
arrayQualityMetrics(raw_data, intgroup = "Group", outdir = quality_report_path, force = T, showWarnings = F)
Error traceback:
14: file.info(x)
13: length.path(paths)
12: length(paths)
11: grobApply(path, function(path) {
grid.set(path, garnishGrob(grid.get(path), ..., group = group),
redraw = redraw)
}, strict = strict, grep = grep, global = global)
10: grid.garnish(annotationInfo@gridObjId, group = FALSE, grep = TRUE,
class = class, onclick = callbacks[, 1], onmouseover = callbacks[,
2], onmouseout = callbacks[, 3])
9: annotateSvgGrid(annotationInfo = module@svg, name = name)
8: reportModule(p = p, module = modules[[i]], currentIndex = currentIndex,
arrayTable = arrayTableCompact, outdir = outdir)
7: aqm.writereport(modules = m, arrayTable = x$pData, reporttitle = reporttitle,
outdir = outdir)
6: arrayQualityMetrics(raw_data, intgroup = "Group", outdir = quality_report_path,
force = T, showWarnings = F) at quality_control.r#27
5: eval(expr, envir, enclos)
4: eval(ei, envir)
3: withVisible(eval(ei, envir))
2: source("Src/quality_control.r") at pipeline_structure.r#46
1: run_analysis()
Output of sessionInfo():
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)
locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] hgu133plus2probe_2.18.0 hgu133plus2cdf_2.18.0 plotly_2.0.16 ggplot2_2.0.0 WriteXLS_4.0.0
[6] RColorBrewer_1.1-2 gdata_2.17.0 xlsx_0.5.7 xlsxjars_0.6.1 rJava_0.9-8
[11] biomaRt_2.26.1 illuminaHumanv4.db_1.26.0 GEOquery_2.36.0 lumi_2.22.1 pd.huex.1.0.st.v2_3.14.1
[16] oligoData_1.8.0 oligo_1.34.2 Biostrings_2.38.4 XVector_0.10.0 oligoClasses_1.32.0
[21] hgu133a.db_3.2.2 annaffy_1.42.0 GO.db_3.2.2 affyQCReport_1.48.0 lattice_0.20-33
[26] affycoretools_1.42.0 affyPLM_1.46.0 preprocessCore_1.32.0 simpleaffy_2.46.0 gcrma_2.42.0
[31] genefilter_1.52.1 affy_1.48.0 hgu133plus2.db_3.2.2 stringr_1.0.0 pathview_1.10.1
[36] org.Hs.eg.db_3.2.3 KEGG.db_3.2.2 RSQLite_1.0.0 DBI_0.3.1 AnnotationDbi_1.32.3
[41] IRanges_2.4.8 S4Vectors_0.8.11 Biobase_2.30.0 BiocGenerics_0.16.1 limma_3.26.8
[46] arrayQualityMetrics_3.26.1 BiocInstaller_1.20.1
loaded via a namespace (and not attached):
[1] R.utils_2.2.0 htmlwidgets_0.6 beadarray_2.20.1 grid_3.2.2 BiocParallel_1.4.3
[6] munsell_0.4.3 codetools_0.2-14 nleqslv_3.0 colorspace_1.2-6 BiocInstaller_1.20.1
[11] Category_2.36.0 OrganismDbi_1.12.1 knitr_1.12.3 setRNG_2013.9-1 KEGGgraph_1.28.0
[16] hwriter_1.3.2 lambda.r_1.1.7 biovizBase_1.18.0 affxparser_1.42.0 R6_2.1.2
[21] GenomeInfoDb_1.6.3 illuminaio_0.12.0 gridSVG_1.5-1 RJSONIO_1.3-0 locfit_1.5-9.1
[26] bitops_1.0-6 reshape_0.8.5 RcppArmadillo_0.6.500.4.0 scales_0.4.0 nnet_7.3-12
[31] gtable_0.2.0 Cairo_1.5-9 methylumi_2.16.0 ggbio_1.18.5 splines_3.2.2
[36] rtracklayer_1.30.2 acepack_1.3-3.3 dichromat_2.0-0 rgl_0.95.1441 reshape2_1.4.1
[41] SVGAnnotation_0.93-1 GenomicFeatures_1.22.13 Hmisc_3.17-2 RBGL_1.46.0 tools_3.2.2
[46] nor1mix_1.2-1 affyio_1.40.0 gplots_2.17.0 ff_2.2-13 siggenes_1.44.0
[51] Rcpp_0.12.3 plyr_1.8.3 base64enc_0.1-3 zlibbioc_1.16.0 RCurl_1.95-4.8
[56] rpart_4.1-10 viridis_0.3.2 bumphunter_1.10.0 SummarizedExperiment_1.0.2 cluster_2.0.3
[61] magrittr_1.5 futile.options_1.0.0 matrixStats_0.50.1 xtable_1.8-2 XML_3.98-1.4
[66] mclust_5.1 gridExtra_2.2.1 ellipse_0.3-8 minfi_1.16.1 KernSmooth_2.23-15
[71] htmltools_0.3 ReportingTools_2.10.0 R.oo_1.20.0 GOstats_2.36.0 mgcv_1.8-11
[76] corpcor_1.6.8 Formula_1.2-1 geneplotter_1.48.0 MASS_7.3-45 Matrix_1.2-3
[81] vsn_3.38.0 quadprog_1.5-5 R.methodsS3_1.7.1 igraph_1.0.1 GenomicRanges_1.22.4
[86] GenomicAlignments_1.6.3 registry_0.3 foreign_0.8-66 foreach_1.4.3 annotate_1.48.0
[91] BeadDataPackR_1.22.0 rngtools_1.2.4 pkgmaker_0.22 multtest_2.26.0 beanplot_1.2
[96] AnnotationForge_1.12.2 doRNG_1.6 VariantAnnotation_1.16.4 digest_0.6.9 graph_1.48.0
[101] base64_1.1 edgeR_3.12.0 GSEABase_1.32.0 Rsamtools_1.22.0 gtools_3.5.0
[106] jsonlite_0.9.19 nlme_3.1-125 PFAM.db_3.2.2 mixOmics_5.2.0 futile.logger_1.4.1
[111] BSgenome_1.38.0 GGally_1.0.1 KEGGREST_1.10.1 httr_1.1.0 survival_2.38-3
[116] png_0.1-7 iterators_1.0.8 bit_1.1-12 Rgraphviz_2.14.0 stringi_1.0-1
[121] DESeq2_1.10.1 latticeExtra_0.6-28 caTools_1.17.1
Is anybody experiencing the same problems? Hope someone can help.
Best regards,
Jan-Niklas
I'm getting the same error.