[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:
>smooth
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,
Fides
-- output of sessionInfo():
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[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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