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Question: arrayQualityMetrics in reading HTAfeatureSet read by oligo package
gravatar for RV
11 weeks ago by
RV10 wrote:


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 

ADD COMMENTlink modified 10 weeks ago by Mike Smith3.2k • written 11 weeks ago by RV10

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.

ADD REPLYlink written 11 weeks ago by Mike Smith3.2k

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. 



ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by RV10
Answer: arrayQualityMetrics in reading HTAfeatureSet read by oligo package
gravatar for Mike Smith
10 weeks ago by
Mike Smith3.2k
EMBL Heidelberg / de.NBI
Mike Smith3.2k wrote:

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)))
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Mike Smith3.2k

Hi Mike, 

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


ADD REPLYlink written 10 weeks ago by RV10
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