[BioC] arrayQualityMetrics does not produce interactive plots

Steven Cowman [guest] guest at bioconductor.org
Tue Oct 8 14:21:52 CEST 2013


Dear all,

This is my first posting and I apologise for any errors or missing information.

I am having trouble with arrayQualityMetrics interactive plots, which produce the following error message (within the index.html report):

"Note: the figure is static - enhancement with interactive effects failed. This is either due to a version incompatibility of the 'SVGAnnotation' R package and your version of 'Cairo' or 'libcairo', or due to plot misformating. Please consult the Bioconductor mailing list, or contact the maintainer of 'arrayQualityMetrics' with a reproducible example in order to fix this problem."

After reading the previous posting about this problem (https://stat.ethz.ch/pipermail/bioconductor/2011-December/042454.html) I updated Cairo and libxml2 using Macports (I am using a MacBook Pro with OSX 10.8.4 and Safari as my web browser) but the problem persists. All my installed packages are up-to-date.

I have tried give a replicable example of my problem using "golubEsets" as the expression data and have attached a print-out of the session below.

I would be very grateful for any help or advice anyone can provide,

Best wishes,

Steven


R version 3.0.1 (2013-05-16) -- "Good Sport"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (64-bit)

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  Natural language support but running in an English locale

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library("arrayQualityMetrics")
Creating a generic function for ‘boxplot’ from package ‘graphics’ in package ‘affyPLM’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
> library("golubEsets")
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap,
    parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find, get,
    intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unlist

Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

> data(Golub_Train)
> Outputdir <- "/Users/mydirectory/array Quality Metrics/"
> arrayQualityMetrics(Golub_Train, outdir=Outputdir)
The directory '/Users/mydirectory/array Quality Metrics/' has been created.
Error in tmp[i] : invalid subscript type 'list'
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning messages:
1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
2: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
3: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
4: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
5: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
6: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] golubEsets_1.4.13          Biobase_2.20.1             BiocGenerics_0.6.0        
[4] arrayQualityMetrics_3.16.0

loaded via a namespace (and not attached):
 [1] affy_1.38.1           affyio_1.28.0         affyPLM_1.36.0        annotate_1.38.0      
 [5] AnnotationDbi_1.22.6  beadarray_2.10.0      BeadDataPackR_1.12.0  BiocInstaller_1.10.3 
 [9] Biostrings_2.28.0     Cairo_1.5-2           cluster_1.14.4        colorspace_1.2-3     
[13] DBI_0.2-7             gcrma_2.32.0          genefilter_1.42.0     grid_3.0.1           
[17] Hmisc_3.12-2          hwriter_1.3           IRanges_1.18.4        KernSmooth_2.23-10   
[21] lattice_0.20-23       latticeExtra_0.6-26   limma_3.16.8          plyr_1.8             
[25] preprocessCore_1.22.0 RColorBrewer_1.0-5    reshape2_1.2.2        rpart_4.1-3          
[29] RSQLite_0.11.4        setRNG_2011.11-2      splines_3.0.1         stats4_3.0.1         
[33] stringr_0.6.2         survival_2.37-4       SVGAnnotation_0.93-1  tools_3.0.1          
[37] vsn_3.28.0            XML_3.95-0.2          xtable_1.7-1          zlibbioc_1.6.0  

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