Entering edit mode
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
