DiffBind error during normalization
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jseg • 0
@4cfcb545
Last seen 17 hours ago
France

Hi all,

I'm using DiffBind 3.2.14 with spike-in data. I have an issue when running dba.normalize(). The error seems to be coming from the minQCth argument.

I'm providing here the code I run to create my DBA object as well as the error messages I get and the traceback.

Furthermore, I provide the content of the dbObj2$config$minQCth that are not what I set them to be (a vector of 15,15 instead of a scalar of 15).

Does the problem come from my config and how can I get rid of it ?

Thank you for your time,

Best wishes.


dbObj <- dba(sampleSheet = "samples.csv", skipLines=1, bRemoveM=TRUE, bRemoveRandom=TRUE,
            config=data.frame(AnalysisMethod=DBA_DESEQ2, th=0.01,
                             DataType=DBA_DATA_GRANGES, RunParallel=TRUE,
                             minQCth=15, bCorPlot=TRUE, ReportInit="DB_output", 
                             bUsePval=FALSE, design=TRUE, doBlacklist=TRUE, 
                             doGreylist=TRUE))

dbObj1 <- dba.blacklist(dbObj)

dbObj2 <- dba.count(dbObj1, bUseSummarizeOverlaps = TRUE)

dbObj3 <- dba.normalize(dbObj2, method=DBA_ALL_METHODS, normalize=DBA_NORM_NATIVE, spikein=TRUE)

Generating counts for spike-ins...
Error in validObject(.Object) : 
  invalid class “readParam” object: minimum mapping quality must be a numeric scalar
In addition: Warning message:
In if (DBA$config$design == FALSE) { :
  the condition has length > 1 and only the first element will be used


traceback()
10: stop(msg, ": ", errors, domain = NA)
9: validObject(.Object)
8: initialize(value, ...)
7: initialize(value, ...)
6: new("readParam", pe = pe, max.frag = max.frag, dedup = dedup, 
       forward = forward, minq = minq, restrict = restrict, discard = discard, 
       processed.discard = .setupDiscard(discard))
5: csaw::readParam(pe = pe, minq = minq)
4: pv.readParams(pv, restrict)
3: pv.getBackground(pv, background, spikein)
2: pv.normalize(DBA, method = method, libSizes = library, normalize = normalize, 
       libFun = libFun, background = background, spikein = spikein, 
       offsets = offsets, bRetrieve = bRetrieve, filter = 0, ...)
1: dba.normalize(dbObj2, method = DBA_ALL_METHODS, normalize = DBA_NORM_NATIVE, 
       spikein = TRUE)


dbObj2$config$minQCth
[1] 15 15

dbObj2$config$mapQCth
[1] 15

###############################

###############################
sessionInfo( )
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bullseye/sid

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.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] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] DiffBind_3.2.4              SummarizedExperiment_1.22.0
 [3] Biobase_2.52.0              MatrixGenerics_1.4.0       
 [5] matrixStats_0.60.0          GenomicRanges_1.44.0       
 [7] GenomeInfoDb_1.28.1         IRanges_2.26.0             
 [9] S4Vectors_0.30.0            BiocGenerics_0.38.0        

loaded via a namespace (and not attached):
  [1] backports_1.2.1          GOstats_2.58.0           BiocFileCache_2.0.0     
  [4] plyr_1.8.6               GSEABase_1.54.0          splines_4.1.0           
  [7] BiocParallel_1.26.1      ggplot2_3.3.5            amap_0.8-18             
 [10] digest_0.6.27            invgamma_1.1             GO.db_3.13.0            
 [13] SQUAREM_2021.1           fansi_0.5.0              csaw_1.26.0             
 [16] magrittr_2.0.1           checkmate_2.0.0          memoise_2.0.0           
 [19] BSgenome_1.60.0          base64url_1.4            limma_3.48.1            
 [22] Biostrings_2.60.1        annotate_1.70.0          systemPipeR_1.26.3      
 [25] bdsmatrix_1.3-4          prettyunits_1.1.1        jpeg_0.1-9              
 [28] colorspace_2.0-2         blob_1.2.2               rappdirs_0.3.3          
 [31] apeglm_1.14.0            ggrepel_0.9.1            dplyr_1.0.7             
 [34] crayon_1.4.1             RCurl_1.98-1.3           jsonlite_1.7.2          
 [37] graph_1.70.0             genefilter_1.74.0        brew_1.0-6              
 [40] survival_3.2-7           VariantAnnotation_1.38.0 glue_1.4.2              
 [43] gtable_0.3.0             zlibbioc_1.38.0          XVector_0.32.0          
 [46] DelayedArray_0.18.0      V8_3.4.2                 Rgraphviz_2.36.0        
 [49] scales_1.1.1             pheatmap_1.0.12          mvtnorm_1.1-2           
 [52] DBI_1.1.1                edgeR_3.34.0             Rcpp_1.0.7              
 [55] xtable_1.8-4             progress_1.2.2           emdbook_1.3.12          
 [58] bit_4.0.4                rsvg_2.1.2               AnnotationForge_1.34.0  
 [61] truncnorm_1.0-8          metapod_1.0.0            httr_1.4.2              
 [64] gplots_3.1.1             RColorBrewer_1.1-2       ellipsis_0.3.2          
 [67] pkgconfig_2.0.3          XML_3.99-0.6             dbplyr_2.1.1            
 [70] locfit_1.5-9.4           utf8_1.2.2               tidyselect_1.1.1        
 [73] rlang_0.4.11             AnnotationDbi_1.54.1     munsell_0.5.0           
 [76] tools_4.1.0              cachem_1.0.5             generics_0.1.0          
 [79] RSQLite_2.2.7            stringr_1.4.0            fastmap_1.1.0           
 [82] yaml_2.2.1               bit64_4.0.5              caTools_1.18.2          
 [85] purrr_0.3.4              KEGGREST_1.32.0          RBGL_1.68.0             
 [88] xml2_1.3.2               biomaRt_2.48.2           compiler_4.1.0          
 [91] rstudioapi_0.13          filelock_1.0.2           curl_4.3.2              
 [94] png_0.1-7                tibble_3.1.3             stringi_1.7.3           
 [97] GenomicFeatures_1.44.0   lattice_0.20-41          Matrix_1.3-2            
[100] vctrs_0.3.8              pillar_1.6.2             lifecycle_1.0.0         
[103] irlba_2.3.3              data.table_1.14.0        bitops_1.0-7            
[106] rtracklayer_1.52.0       R6_2.5.0                 BiocIO_1.2.0            
[109] latticeExtra_0.6-29      hwriter_1.3.2            ShortRead_1.50.0        
[112] KernSmooth_2.23-18       MASS_7.3-53.1            gtools_3.9.2            
[115] assertthat_0.2.1         Category_2.58.0          rjson_0.2.20            
[118] withr_2.4.2              GenomicAlignments_1.28.0 batchtools_0.9.15       
[121] Rsamtools_2.8.0          GenomeInfoDbData_1.2.6   hms_1.1.0               
[124] grid_4.1.0               DOT_0.1                  coda_0.19-4             
[127] GreyListChIP_1.24.0      ashr_2.2-47              mixsqp_0.3-43           
[130] bbmle_1.0.23.1           numDeriv_2016.8-1.1      restfulr_0.0.13
DiffBind • 105 views
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