[BioC] Error using Bsmooth.tstat due to NAs

[Kasper Daniel Hansen]

This is hard to know for sure without knowing much more about the data.

My guess is that you have some contigs (chromosomes) which are super small
and they cause problems.  You can also try setting verbose to say 2 or 3
and see if that helps narrow down where in the function it happens.

On Wed, Sep 10, 2014 at 12:18 PM, Fides Lay [guest] <guest at bioconductor.org>
wrote:

> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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