Question: error in TCseq
0
gravatar for k.panov
14 months ago by
k.panov0
k.panov0 wrote:

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
tcseq • 229 views
ADD COMMENTlink written 14 months ago by k.panov0
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