Hello, Rory, Thank you for suggestions at C: Warnings when update DiffBind and running errors. I still failed run with dba.count, however. Here is what I have done.
1. I have update all the packages. when loading Diffbind 2.6, there is no warnings.
2. Then I run dba.count using summits=150 with score default. the error came out again. How could I fix it?
Error in heights * sapply(called, function(x) x) : non-conformable arrays
Many Thanks
Zhaolin
> library(DiffBind) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel
Attaching package: âBiocGenericsâ
The following objects are masked from âpackage:parallelâ:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from âpackage:statsâ:
IQR, mad, sd, var, xtabs
The following objects are masked from âpackage:baseâ:
anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: âS4Vectorsâ
The following object is masked from âpackage:baseâ:
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: âmatrixStatsâ
The following objects are masked from âpackage:Biobaseâ:
anyMissing, rowMedians
Attaching package: âDelayedArrayâ
The following objects are masked from âpackage:matrixStatsâ:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from âpackage:baseâ:
apply
> eiff<-dba(sampleSheet="090217_3_CD4.csv",config=data.frame(RunParallel=TRUE, reportInit="eiff",AnalysisMethod=DBA_DESEQ2,th=0.05)) >eiff1<-dba.count(eiff, minOverlap=12,summits=150,readFormat=DBA_READS_DEFAULT, bParallel=eiff$config$RunParallel)
Re-centering peaks...
Error in heights * sapply(called, function(x) x) : non-conformable arrays
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/lapack/liblapack.so.3.0
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_2.6.1 SummarizedExperiment_1.8.0
[3] DelayedArray_0.4.1 matrixStats_0.52.2
[5] Biobase_2.38.0 GenomicRanges_1.30.0
[7] GenomeInfoDb_1.14.0 IRanges_2.12.0
[9] S4Vectors_0.16.0 BiocGenerics_0.24.0
loaded via a namespace (and not attached):
[1] Category_2.44.0 bitops_1.0-6 bit64_0.9-7
[4] RColorBrewer_1.1-2 progress_1.1.2 Rgraphviz_2.22.0
[7] tools_3.4.2 backports_1.1.1 R6_2.2.2
[10] KernSmooth_2.23-15 DBI_0.7 lazyeval_0.2.1
[13] colorspace_1.3-2 prettyunits_1.0.2 RMySQL_0.10.13
[16] bit_1.1-12 compiler_3.4.2 sendmailR_1.2-1
[19] graph_1.56.0 rtracklayer_1.38.0 caTools_1.17.1
[22] scales_0.5.0 checkmate_1.8.5 BatchJobs_1.7
[25] genefilter_1.60.0 RBGL_1.54.0 stringr_1.2.0
[28] digest_0.6.12 Rsamtools_1.30.0 AnnotationForge_1.20.0
[31] XVector_0.18.0 base64enc_0.1-3 pkgconfig_2.0.1
[34] limma_3.34.2 rlang_0.1.4 RSQLite_2.0
[37] BBmisc_1.11 BiocInstaller_1.28.0 bindr_0.1
[40] GOstats_2.44.0 hwriter_1.3.2 BiocParallel_1.10.1
[43] gtools_3.5.0 dplyr_0.7.4 RCurl_1.95-4.8
[46] magrittr_1.5 GO.db_3.5.0 GenomeInfoDbData_0.99.1
[49] Matrix_1.2-12 Rcpp_0.12.14 munsell_0.4.3
[52] stringi_1.1.6 edgeR_3.18.1 zlibbioc_1.24.0
[55] gplots_3.0.1 plyr_1.8.4 grid_3.4.2
[58] blob_1.1.0 ggrepel_0.7.0 gdata_2.18.0
[61] lattice_0.20-35 Biostrings_2.46.0 splines_3.4.2
[64] GenomicFeatures_1.30.0 annotate_1.56.1 locfit_1.5-9.1
[67] rjson_0.2.15 systemPipeR_1.12.0 biomaRt_2.34.0
[70] glue_1.2.0 XML_3.98-1.9 ShortRead_1.36.0
[73] latticeExtra_0.6-28 data.table_1.10.4-3 gtable_0.2.0
[76] amap_0.8-14 assertthat_0.2.0 ggplot2_2.2.1
[79] xtable_1.8-2 survival_2.41-3 tibble_1.3.4
[82] pheatmap_1.0.8 GenomicAlignments_1.14.1 AnnotationDbi_1.40.0
[85] memoise_1.1.0 bindrcpp_0.2 brew_1.0-6
[88] GSEABase_1.40.1
Hi Zhaolin,
I ran into the same error message while running DiffBind. Did you happen to figure out the reason and/or a fix?
Thanks for your help!
Ashu