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Hello, I have following error message when I run TCseq 3.6 package:
> tca <- DBanalysis(tca)
Error in .compressDispersions(y, dispersion) :
dispersions must be finite non-negative values
In addition: Warning message:
In estimateDisp.default(y = y$counts, design = design, group = group, :
No residual df: setting dispersion to NA
Any suggestions why? (below on outcome of tca and session info)
> tca
An object of class "TCA"
@design
sampleid timepoint group BAMfile
1 SS.1 0min 1 ss_m.bam
2 rf15.1 15min 2 rf15_m.bam
3 rf30.1 30min 3 rf30_m.bam
4 rf120.1 120min 4 rf120_m.bam
5 AG.1 600min 5 ag_m.bam
@counts
ss_m.bam rf15_m.bam rf30_m.bam rf120_m.bam ag_m.bam
peak1 250 309 212 362 175
peak2 26 14 12 17 20
peak3 188 142 121 266 164
peak4 179 165 149 192 105
peak5 3 5 7 11 31
42620 more rows ...
@genomicFeature
chr start end id
1 1 29310 29702 peak1
2 1 133197 133413 peak2
3 1 778457 779280 peak3
4 1 826973 827957 peak4
5 1 850317 850516 peak5
42620 more rows ...
@clusterRes
An object of class "clust"
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] TCseq_1.2.0 BiocInstaller_1.28.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 compiler_3.4.3 pillar_1.2.1
[4] GenomeInfoDb_1.14.0 plyr_1.8.4 XVector_0.18.0
[7] bitops_1.0-6 class_7.3-14 tools_3.4.3
[10] zlibbioc_1.24.0 tibble_1.4.2 gtable_0.2.0
[13] lattice_0.20-35 rlang_0.2.0 Matrix_1.2-12
[16] DelayedArray_0.4.1 yaml_2.1.18 parallel_3.4.3
[19] GenomeInfoDbData_1.0.0 e1071_1.6-8 stringr_1.3.0
[22] cluster_2.0.6 Biostrings_2.46.0 S4Vectors_0.16.0
[25] IRanges_2.12.0 stats4_3.4.3 locfit_1.5-9.1
[28] grid_3.4.3 Biobase_2.38.0 snow_0.4-2
[31] BiocParallel_1.12.0 limma_3.34.9 magrittr_1.5
[34] ggplot2_2.2.1 reshape2_1.4.3 edgeR_3.20.9
[37] Rsamtools_1.30.0 GenomicAlignments_1.14.1 scales_0.5.0
[40] matrixStats_0.53.1 BiocGenerics_0.24.0 GenomicRanges_1.30.3
[43] SummarizedExperiment_1.8.1 colorspace_1.3-2 stringi_1.1.7
[46] RCurl_1.95-4.10 lazyeval_0.2.1 munsell_0.4.3