[BioC] flowStats's warping function problem
cwon2 at fhcrc.org
Fri Oct 9 21:24:20 CEST 2009
The first error message that you got is quite common when using the
flowStats' warping function. I post your question on the mailing list so
that other people can benefit from it.
The first issue is due to a floating point problem in the fda package
that we use for wrapping the data. Spancer Graves (fda's maintainer) has
fixed it in version 2.1.3 which will appear in the newly-released R.
2.10 in the end of this month. Unfortunately, I was not able to find the
binary file of fad_2.1.3.tar.gz on line. What I can do now is that I can
wrap the fda package that I modified and email to you. What do you think?
As for the second issue, it seems to me that the data object might be
empty. Anyhow, I will take a look at your data and will get back to you
> Hi guys,
> I am experiencing some weird behavior when running the warpSet function
> (flowStats 1.3.19)
> The flowSet that I am using is attached.
> Issue 1, error:
> > warpSet(original, "FSC-H")$flowset
> Estimating landmarks for channel FSC-H ...
> Registering curves for parameter FSC-H ...
> Error in seq.default(rangeval + del/2, rangeval - del/2, del) :
> wrong sign in 'by' argument
> Issue 2, no error but returns NULL:
> > warpSet(original, "FL1-H")$flowset
> Estimating landmarks for channel FL1-H ...
> Registering curves for parameter FL1-H ...
> This is my configuration:
> > sessionInfo()
> R version 2.10.0 alpha (2009-10-06 r49961) x86_64-unknown-linux-gnu
>  LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
>  LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
>  LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8
>  LC_PAPER=en_CA.UTF-8 LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  splines stats graphics grDevices utils datasets methods
>  base
> other attached packages:
>  flowViz_1.9.9 lattice_0.17-26 flowStats_1.3.19 mvoutlier_1.4
>  fda_2.1.2 zoo_1.5-8 flowCore_1.11.22 rrcov_0.5-02
>  pcaPP_1.7 mvtnorm_0.9-7 robustbase_0.4-5 Biobase_2.5.8
> loaded via a namespace (and not attached):
>  feature_1.2.4 graph_1.23.7 grid_2.10.0
>  ks_1.6.7 latticeExtra_0.6-1 MASS_7.3-2
>  stats4_2.10.0 tools_2.10.0
> Am I just applying it in a stupid way or is there a bug?
> Josef Spidlen, Ph.D.
> Terry Fox Laboratory, BC Cancer Agency
> 675 West 10th Avenue, V5Z 1L3 Vancouver, BC, Canada
> Tel: +1 (604) 675-8000 x 7755
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M2-B876
PO Box 19024
Seattle, WA 98109
cwon2 at fhcrc.org
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