centeredSampleClustering fails when all samples are flagged
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@gregory-warnes-2155
Last seen 7.7 years ago
United States

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           
NanoStringQCPro • 845 views
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