I am processing a NanoString data set where all of the samples fail the 20% Gene detection count test. (The NanoString kit contains only a few genes that applicable to the cells being processed.)
In this case, running makeQCReport fails in centeredSampleClustering with the error :
Generating QC report...
Gene-wise counts in blank samples: main image...
[1] "No blank samples are present"
Gene-wise counts in blank samples: preview image...
[1] "Input file not found"
Negative controls by lane: main image...
Negative controls by lane: preview image...
Raw and content normalized data for density plots and gene clustering...
Heatmaps...
Sample clustering: main image...
Sample clustering: preview image...
Gene clustering (global normalization): main image...
Gene clustering (global normalization): preview image...
Gene clustering (housekeeping normalization): main image...
Gene clustering (housekeeping normalization): preview image...
Centered sample clustering: main image...
Centered sample clustering: preview image...
Centered sample clustering (excluding flagged samples): main image...
Error in `rownames<-`(`*tmp*`, value = c("C4BPA", "C7", "CASP10", "PBK", :
length of 'dimnames' [1] not equal to array extent
I've created a pull request in github that modifies centeredSampleClustering to generate an empty plot containing the text "All samples are flagged./nNo Samples to Plot." and the warning "All samples are flagged. Generating empty plot.".
The commit to my fork of the NanoStringQCPro repo is at https://github.com/warnes/NanoStringQCPro/commit/47f76ace9ed9597f9f461cf7f9d6557843b1fc3e
The pull request is at:https://github.com/Bioconductor-mirror/NanoStringQCPro/pull/1
(Session Info below.)
-Greg
> sessionInfo()
R version 3.2.0 (2015-04-16) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Scientific Linux release 6.6 (Carbon) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] RColorBrewer_1.1-2 gplots_3.0.2 BIexpr_1.0 car_2.0-25 devtools_1.8.0 NanoStringQCPro_1.4.0 [7] synchronicity_1.1.9.1 bigmemory_4.5.19 bigmemory.sri_0.1.3 Biobase_2.30.0 BiocGenerics_0.16.1 RSQLite_1.0.0 [13] DBI_0.3.1 matrixStats_0.50.1 edgeR_3.12.0 limma_3.26.3 openxlsx_3.0.0 d3heatmap_0.6.1.1 [19] gtools_3.5.0 gdata_2.17.0 knitr_1.13 pander_0.6.0 loaded via a namespace (and not attached): [1] splines_3.2.0 foreach_1.4.2 stats4_3.2.0 yaml_2.1.13 lattice_0.20-33 quantreg_5.11 [7] digest_0.6.9 minqa_1.2.4 colorspace_1.2-6 htmltools_0.3.5 Matrix_1.2-2 plyr_1.8.3 [13] SparseM_1.6 xtable_1.8-0 scales_0.4.0 lme4_1.1-8 git2r_0.13.1 pkgmaker_0.22 [19] mgcv_1.8-6 IRanges_2.4.6 ggplot2_2.1.0 nnet_7.3-11 pbkrtest_0.4-2 magrittr_1.5 [25] evaluate_0.9 memoise_1.0.0 doParallel_1.0.8 nlme_3.1-121 MASS_7.3-45 NMF_0.20.6 [31] xml2_0.1.1 rsconnect_0.3.79 tools_3.2.0 registry_0.3 org.Hs.eg.db_3.1.2 gridBase_0.4-7 [37] stringr_1.0.0 S4Vectors_0.8.5 munsell_0.4.2 cluster_2.0.3 rngtools_1.2.4 AnnotationDbi_1.32.3 [43] rversions_1.0.1 caTools_1.17.1 grid_3.2.0 nloptr_1.0.4 iterators_1.0.7 htmlwidgets_0.6 [49] bitops_1.0-6 base64enc_0.1-3 rmarkdown_0.9.6 gtable_0.1.2 codetools_0.2-14 roxygen2_4.1.1 [55] curl_0.9.7 reshape2_1.4.1 KernSmooth_2.23-15 stringi_1.0-1 Rcpp_0.12.5 png_0.1-7
