Question: Arrayquality metrics Warning - Warning message in maximumLevels(fac, n = length(colors)):
0
gravatar for RV
5 months ago by
RV10
RV10 wrote:

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 - https://stat.ethz.ch/pipermail/bioconductor/2014-May/059860.html

Thanks!

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/libopenblasp-r0.3.3.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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
microarray wolfgang huber • 175 views
ADD COMMENTlink written 5 months ago by RV10
1

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.

ADD REPLYlink written 5 months ago by Mike Smith3.8k

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.

ADD REPLYlink modified 5 months ago • written 5 months ago by RV10

The warning message you quote cannot have been generated from a recent version of arrayQualityMetrics, see e.g. https://github.com/grimbough/arrayQualityMetrics/blob/master/R/makeColors.R. Are you sure you are not using an older version of the package?

ADD REPLYlink written 5 months ago by Wolfgang Huber13k
1

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.

ADD REPLYlink written 5 months ago by Mike Smith3.8k
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