Arrayquality metrics Warning - Warning message in maximumLevels(fac, n = length(colors)):
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RV ▴ 10
Last seen 2.8 years ago

Hi Wolfgang, I am using ArrayQuality metrics for more than 1300 samples and I get a warning - Warning message in maximumLevels(fac, n = length(colors)): "A factor was provided with 16 levels, but the colour map used here has only 9 colours. For the purpose of colouring, levels 9 ('1031863') to 16 ('1032012') are being collapsed. Please consider grouping together some of the levels of your factor of interest to reduce the number of levels, this might improve the legibility of the plots.

I saw another comment that had requested in increase in color, 5 years back and the answer you had given was to download the latest. Does it still work ?

Here is the comment -


R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

Matrix products: default
BLAS/LAPACK: /home/linuxbrew/.linuxbrew/Cellar/openblas/0.3.3/lib/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] FactoMineR_1.41            affycoretools_1.54.0      
 [3] pd.hta.2.0_3.12.2          DBI_1.0.0                 
 [5] RSQLite_2.1.1              genefilter_1.64.0         
 [7] limma_3.38.3               oligo_1.46.0              
 [9] Biostrings_2.50.2          XVector_0.22.0            
[11] IRanges_2.16.0             S4Vectors_0.20.1          
[13] Biobase_2.42.0             oligoClasses_1.44.0       
[15] BiocGenerics_0.28.0        arrayQualityMetrics_3.38.0

loaded via a namespace (and not attached):
  [1] uuid_0.1-2                  backports_1.1.3            
  [3] GOstats_2.48.0              Hmisc_4.1-1                
  [5] plyr_1.8.4                  repr_0.19.1                
  [7] lazyeval_0.2.1              GSEABase_1.44.0            
  [9] splines_3.5.1               BiocParallel_1.16.5        
 [11] GenomeInfoDb_1.18.1         ggplot2_3.1.0              
 [13] digest_0.6.18               ensembldb_2.6.3            
 [15] foreach_1.4.4               htmltools_0.3.6            
 [17] GO.db_3.7.0                 gdata_2.18.0               
 [19] magrittr_1.5                checkmate_1.9.1            
 [21] memoise_1.1.0               BSgenome_1.50.0            
 [23] affyPLM_1.58.0              cluster_2.0.7-1            
 [25] gcrma_2.54.0                annotate_1.60.0            
 [27] matrixStats_0.54.0          beadarray_2.32.0           
 [29] R.utils_2.7.0               ggbio_1.30.0               
 [31] askpass_1.1                 prettyunits_1.0.2          
 [33] colorspace_1.4-0            blob_1.1.1                 
 [35] xfun_0.4                    dplyr_0.7.8                
 [37] crayon_1.3.4                RCurl_1.95-4.11            
 [39] jsonlite_1.6                graph_1.60.0               
 [41] bindr_0.1.1                 VariantAnnotation_1.28.10  
 [43] survival_2.43-3             iterators_1.0.10           
 [45] glue_1.3.0                  gtable_0.2.0               
 [47] zlibbioc_1.28.0             DelayedArray_0.8.0         
 [49] BeadDataPackR_1.34.0        Rgraphviz_2.26.0           
 [51] scales_1.0.0                setRNG_2013.9-1            
 [53] vsn_3.50.0                  GGally_1.4.0               
 [55] edgeR_3.24.3                Rcpp_1.0.0                 
 [57] xtable_1.8-3                progress_1.2.0             
 [59] htmlTable_1.13.1            flashClust_1.01-2          
 [61] foreign_0.8-71              bit_1.1-14                 
 [63] OrganismDbi_1.24.0          preprocessCore_1.44.0      
 [65] Formula_1.2-3               AnnotationForge_1.24.0     
 [67] httr_1.4.0                  htmlwidgets_1.3            
 [69] gplots_3.0.1                RColorBrewer_1.1-2         
 [71] acepack_1.4.1               ff_2.2-14                  
 [73] R.methodsS3_1.7.1           pkgconfig_2.0.2            
 [75] reshape_0.8.8               XML_3.98-1.16              
 [77] nnet_7.3-12                 locfit_1.5-9.1             
 [79] tidyselect_0.2.5            rlang_0.3.1                
 [81] reshape2_1.4.3              AnnotationDbi_1.44.0       
 [83] munsell_0.5.0               tools_3.5.1                
 [85] evaluate_0.12               stringr_1.3.1              
 [87] knitr_1.21                  bit64_0.9-7                
 [89] caTools_1.17.1.1            purrr_0.2.5                
 [91] AnnotationFilter_1.6.0      bindrcpp_0.2.2             
 [93] RBGL_1.58.1                 R.oo_1.22.0                
 [95] leaps_3.0                   biomaRt_2.38.0             
 [97] compiler_3.5.1              rstudioapi_0.9.0           
 [99] curl_3.3                    affyio_1.52.0              
[101] PFAM.db_3.7.0               tibble_2.0.1               
[103] geneplotter_1.60.0          stringi_1.2.4              
[105] GenomicFeatures_1.34.1      lattice_0.20-38            
[107] IRdisplay_0.7.0             ProtGenerics_1.14.0        
[109] Matrix_1.2-15               pillar_1.3.1               
[111] BiocManager_1.30.4          data.table_1.12.0          
[113] bitops_1.0-6                rtracklayer_1.42.1         
[115] GenomicRanges_1.34.0        R6_2.3.0                   
[117] latticeExtra_0.6-28         affy_1.60.0                
[119] hwriter_1.3.2               KernSmooth_2.23-15         
[121] gridSVG_1.6-0               gridExtra_2.3              
[123] affxparser_1.54.0           codetools_0.2-16           
[125] dichromat_2.0-0             MASS_7.3-51.1              
[127] gtools_3.8.1                assertthat_0.2.0           
[129] SummarizedExperiment_1.12.0 openssl_1.2.1              
[131] DESeq2_1.22.2               Category_2.48.0            
[133] ReportingTools_2.22.1       GenomicAlignments_1.18.1   
[135] Rsamtools_1.34.0            GenomeInfoDbData_1.2.0     
[137] hms_0.4.2                   grid_3.5.1                 
[139] rpart_4.1-13                IRkernel_0.8.15            
[141] base64_2.0                  illuminaio_0.24.0          
[143] Cairo_1.5-9                 biovizBase_1.30.1          
[145] pbdZMQ_0.3-3                scatterplot3d_0.3-41       
[147] base64enc_0.1-3
Wolfgang Huber microarray • 489 views
Entering edit mode

Can you provide the call you're making to run arrayQualityMetrics? Taking a look at the code it still looks like the default should still allow up to 17 colours before this warning is generated.

Entering edit mode

Hi Mike,

  arrayQualityMetrics(expressionset = Normdata_1,
                        outdir = paste0("Normdata_1"),
                        force = TRUE, intgroup = c("FUID","PLATE_ID","SCAN_DATE","VISIT","STATE","TRT01A"))

I do not get any error for the last 3 values. The first three variables have 16 levels, each.

This was the call. Thank you for looking into it.

Entering edit mode

The warning message you quote cannot have been generated from a recent version of arrayQualityMetrics, see e.g. Are you sure you are not using an older version of the package?

Entering edit mode

Taking a closer look, this is coming from the aqm.heatmap function where a single colour palette is passed to maximumLevels , so this does happen with the current version. I guess it's not common to encounter more than 9 level in a single covariate, so this doesn't crop up much.


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