arrayQualityMetrics in reading HTAfeatureSet read by oligo package
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RV ▴ 10
Last seen 2.8 years ago


I am trying to perform the standard arrayQualityMetrics for 4 HTA 2.0 CEL files. Following is the code and the error I get. I have pasted the error, traceback and session info. Can you please let me know what I am missing? The CEL files work with all the other package. 





list = list.files(celpath,full.names=TRUE, pattern = "*.CEL", recursive = TRUE)


data = oligo::read.celfiles(list)

arrayQualityMetrics(expressionset = data ,

                    outdir = "Intial_QC",

                    force = TRUE,

                    do.logtransform = TRUE)


The directory 'Intial_QC' has been created.

Error in cpSubsCon(src[k], destname) : UNRESOLVED SYMBOLS:

Line 7 : @52084400103650101719435548086310.CEL", "1" ], [ "2", "@52084400103650101719435548086313.CEL", "2" ], [ "3", "@52084400104783112419435821946312.CEL", "3" ], [ "4", "@5

7: stop(mess)
6: cpSubsCon(src[k], destname)
5: cpSubs(src, dest)
4: copySubstitute(src = filelocs, dest = outdir, recursive = TRUE, 
       symbolValues = params)
3: makeTitle(reporttitle = reporttitle, outdir = outdir, params = c(HIGHLIGHTINITIAL = toJSON_fromchar(ifelse(apply(outliers, 
       1, any), "true", "false")), ARRAYMETADATA = toJSON_frommatrix(arrayTableCompact), 
       SVGOBJECTNAMES = toJSON_fromvector(names(svgdata)), REPORTOBJSTYLES = paste0(".aqm", 
           reportObjs, " { }", collapse = "\n")))
2: aqm.writereport(modules = m, arrayTable = x$pData, reporttitle = reporttitle, 
       outdir = outdir)
1: arrayQualityMetrics(expressionset = data, outdir = "Intial_QC", 
       force = TRUE, do.logtransform = TRUE)


Session info - 

> sessionInfo()
R version 3.5.0 Patched (2018-05-03 r74699)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] pd.hta.2.0_3.12.2          DBI_1.0.0                  RSQLite_2.1.1             
 [4] oligo_1.46.0               Biostrings_2.50.1          XVector_0.22.0            
 [7] IRanges_2.16.0             S4Vectors_0.20.1           Biobase_2.42.0            
[10] oligoClasses_1.44.0        BiocGenerics_0.28.0        arrayQualityMetrics_3.38.0

loaded via a namespace (and not attached):
 [1] bitops_1.0-6                matrixStats_0.54.0          bit64_0.9-7                
 [4] RColorBrewer_1.1-2          GenomeInfoDb_1.18.1         tools_3.5.0                
 [7] backports_1.1.2             gcrma_2.54.0                R6_2.3.0                   
[10] affyio_1.52.0               rpart_4.1-13                Hmisc_4.1-1                
[13] lazyeval_0.2.1              colorspace_1.3-2            nnet_7.3-12                
[16] tidyselect_0.2.5            gridExtra_2.3               base64_2.0                 
[19] bit_1.1-14                  compiler_3.5.0              preprocessCore_1.44.0      
[22] htmlTable_1.12              Cairo_1.5-9                 DelayedArray_0.8.0         
[25] scales_1.0.0                checkmate_1.8.5             genefilter_1.64.0          
[28] affy_1.60.0                 stringr_1.3.1               digest_0.6.18              
[31] foreign_0.8-71              illuminaio_0.24.0           affyPLM_1.58.0             
[34] base64enc_0.1-3             pkgconfig_2.0.2             htmltools_0.3.6            
[37] BeadDataPackR_1.34.0        limma_3.38.2                htmlwidgets_1.3            
[40] rlang_0.3.0.1               rstudioapi_0.8              bindr_0.1.1                
[43] hwriter_1.3.2               jsonlite_1.5                BiocParallel_1.16.0        
[46] acepack_1.4.1               dplyr_0.7.8                 RCurl_1.95-4.11            
[49] magrittr_1.5                GenomeInfoDbData_1.2.0      Formula_1.2-3              
[52] Matrix_1.2-14               Rcpp_1.0.0                  munsell_0.5.0              
[55] vsn_3.50.0                  stringi_1.2.4               SummarizedExperiment_1.12.0
[58] zlibbioc_1.28.0             beadarray_2.32.0            plyr_1.8.4                 
[61] affxparser_1.54.0           grid_3.5.0                  blob_1.1.1                 
[64] crayon_1.3.4                lattice_0.20-35             splines_3.5.0              
[67] annotate_1.60.0             knitr_1.20                  pillar_1.3.0               
[70] GenomicRanges_1.34.0        reshape2_1.4.3              codetools_0.2-15           
[73] XML_3.98-1.16               glue_1.3.0                  latticeExtra_0.6-28        
[76] data.table_1.11.8           BiocManager_1.30.4          foreach_1.4.4              
[79] gtable_0.2.0                openssl_1.0.2               purrr_0.2.5                
[82] assertthat_0.2.0            ggplot2_3.1.0               xtable_1.8-3               
[85] ff_2.2-14                   survival_2.42-6             tibble_1.4.2               
[88] iterators_1.0.10            AnnotationDbi_1.44.0        memoise_1.1.0              
[91] setRNG_2013.9-1             bindrcpp_0.2.2              cluster_2.0.7-1            
[94] gridSVG_1.6-0 

microarray hta2.0 arrayqualitymetrics • 503 views
Entering edit mode

Is it possible for you to save data using the save() function and then share that ExpressionSet object so I can try and debug? I've not seen this error message before.

Entering edit mode

Hi Mike, 

Thanks! Here is the link to the data object. 

Many thanks for looking into it. I am still unable to pinpoint what the reason is. 



Entering edit mode
Mike Smith ★ 5.4k
Last seen 1 day ago
EMBL Heidelberg / de.NBI

I think this is because you have the @ symbol in your file names. arrayQualityMetrics has templates for the reports it produces, with the structure indicated by placeholder entries like @ARRAYNAME@. These are then replaced by the values in the expressionSet when the report is produced.

It's getting confused when the replacement values also have @ symbols and thinks the replacement has failed, hence the error.

I don't think there's a way to change this behaviour, so you can either rename the files themselves or remove the the @ symbols from the file names in the expressionSet. That's what the code below does, and then I am able to run arrayQualityMetrics() successfully.

rownames(phenoData(data)) <- gsub("@", "", rownames(phenoData(data)))
rownames(protocolData(data)) <- gsub("@", "", rownames(protocolData(data)))
Entering edit mode

Hi Mike, 

This is the problem! Thank you so much for helping out. 



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