[BioC] Error using Bsmooth.tstat due to NAs

[Kasper Daniel Hansen]

As Tim Triche pointed out off-list: what you're doing does not make sense
when you only have 1 sample in each group.  I was clearly reading the
report too fast.

On Sun, Sep 14, 2014 at 1:07 PM, Kasper Daniel Hansen <khansen at jhsph.edu>
wrote:

> 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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>
>

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