[BioC] Error using Bsmooth.tstat due to NAs

Fides Lay [guest] guest at bioconductor.org
Wed Sep 10 18:18:10 CEST 2014

Dear all, 

I am trying to use bsseq to analyze WGBS data and identify DMRs following drug treatment. I have a BSseq object consisting of 2 samples (treated and ctrl) that has been smoothed:

An object of type 'BSseq' with
  38250590 methylation loci
  2 samples
has been smoothed with
  BSmooth (ns = 50, h = 500, maxGap = 100000000)

When trying to run BSmooth.tstat, I am encountering the following error due to NAs: 
>smooth=BSmooth.tstat(smooth, group1="Ctrl", group2="Treated", estimate.var="paired", verbose=TRUE, local.correct=TRUE)
preprocessing ... done in 76.1 sec
computing stats within groups ... done in 11.9 sec
computing stats across groups ... Error in approxfun(xx, yy) : 
  need at least two non-NA values to interpolate
Timing stopped at: 7.994 1.649 9.64

However, when I checked in my methylation and coverage matrix, I didn't see any NAs contained in my data, so I am not sure why I am getting this error. 

> summary(getMeth(smooth))
       Ctrl             Treated        
 Min.   :0.0000   Min.   :0.0000  
 1st Qu.:0.6064   1st Qu.:0.3391  
 Median :0.8402   Median :0.4816  
 Mean   :0.7131   Mean   :0.4365  
 3rd Qu.:0.9006   3rd Qu.:0.5600  
 Max.   :1.0000   Max.   :1.0000

I would appreciate any suggestions or advice. 

Thank you very much,

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

[1] C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] bsseqData_0.1.3      bsseq_0.8.0          matrixStats_0.8.14  
[4] GenomicRanges_1.12.5 IRanges_1.18.4       BiocGenerics_0.6.0  
[7] plyr_1.8            

loaded via a namespace (and not attached):
 [1] Biobase_2.20.1     R.methodsS3_1.6.1  RColorBrewer_1.0-5 colorspace_1.2-4  
 [5] dichromat_2.0-0    grid_3.0.1         labeling_0.2       lattice_0.20-24   
 [9] locfit_1.5-9.1     munsell_0.4.2      scales_0.2.3       stats4_3.0.1      
[13] stringr_0.6.2      tools_3.0.1        zlibbioc_1.6.0 

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