Hi,
I changed to R version 3.2.0 and DiffBind version 1.14.3. The problems are:
- The heatmap produced by
data = dba(sampleSheet="HistoneData_C.csv", minOverlap=2)
plot(data)
is different that in previous version that I had (1.8.5) (grouping of samples is different). Is this because of a change in the method or a bug? I tried several versions of parameters.
- The side colours in heatmap do not work - see below.
Would be grateful for solution or explanation.
Best
Pawel
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=Polish_Poland.1250 LC_CTYPE=Polish_Poland.1250 LC_MONETARY=Polish_Poland.1250
[4] LC_NUMERIC=C LC_TIME=Polish_Poland.1250
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] DiffBind_1.14.3 RSQLite_1.0.0 DBI_0.3.1 locfit_1.5-9.1
[5] GenomicAlignments_1.4.1 Rsamtools_1.20.2 Biostrings_2.36.1 XVector_0.8.0
[9] limma_3.24.4 GenomicRanges_1.20.3 GenomeInfoDb_1.4.0 IRanges_2.2.1
[13] S4Vectors_0.6.0 BiocGenerics_0.14.0 BiocInstaller_1.18.2
loaded via a namespace (and not attached):
[1] Rcpp_0.11.6 lattice_0.20-31 GO.db_3.1.2 gtools_3.4.2
[5] digest_0.6.8 plyr_1.8.2 futile.options_1.0.0 BatchJobs_1.6
[9] ShortRead_1.26.0 ggplot2_1.0.1 gplots_2.17.0 zlibbioc_1.14.0
[13] annotate_1.46.0 gdata_2.16.1 Matrix_1.2-0 checkmate_1.5.3
[17] systemPipeR_1.2.1 proto_0.3-10 GOstats_2.34.0 splines_3.2.0
[21] BiocParallel_1.2.1 stringr_1.0.0 pheatmap_1.0.2 munsell_0.4.2
[25] sendmailR_1.2-1 base64enc_0.1-2 BBmisc_1.9 fail_1.2
[29] edgeR_3.10.0 XML_3.98-1.1 AnnotationForge_1.10.1 MASS_7.3-40
[33] bitops_1.0-6 grid_3.2.0 RBGL_1.44.0 xtable_1.7-4
[37] GSEABase_1.30.1 gtable_0.1.2 magrittr_1.5 scales_0.2.4
[41] graph_1.46.0 KernSmooth_2.23-14 amap_0.8-14 stringi_0.4-1
[45] hwriter_1.3.2 reshape2_1.4.1 genefilter_1.50.0 latticeExtra_0.6-26
[49] futile.logger_1.4.1 brew_1.0-6 rjson_0.2.15 lambda.r_1.1.7
[53] RColorBrewer_1.1-2 tools_3.2.0 Biobase_2.28.0 Category_2.34.2
[57] survival_2.38-1 AnnotationDbi_1.30.1 colorspace_1.2-6 caTools_1.17.1
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