[BioC] flowStats's warping function problem

[cwon2 at fhcrc.org]

HI, Josef,

It terms out fda_2.1.3 is available on R-Forge. Quoting from Spencer:

"The current version of fda on R-Forge is 2.1.3 and is available via
install.packages("fda", repos="http://R-Forge.R-project.org")."

I will have submit some examples for testing the modification that  
accounts for the floating point problems before they can release the  
new version. Hopefully it will be done before BioC 2.5's release day.   
Thanks for your patient.

Cheers,
Chao-Jen


Quoting Chao-Jen Wong <cwon2 at fhcrc.org>:

> Hi, Josef,
>
> 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
> soon.
>
> cheers,
> Chao-Jen
>>
>> 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")$flowset
>> Estimating landmarks for channel FSC-H ...
>> Registering curves for parameter FSC-H ...
>> Error in seq.default(rangeval[1] + del/2, rangeval[2] - del/2, del) :
>>   wrong sign in 'by' argument
>>  >
>>
>> Issue 2, no error but returns NULL:
>>  > warpSet(original, "FL1-H")$flowset
>> Estimating landmarks for channel FL1-H ...
>> Registering curves for parameter FL1-H ...
>> NULL
>>  >
>>
>> This is my configuration:
>>  > sessionInfo()
>> R version 2.10.0 alpha (2009-10-06 r49961) x86_64-unknown-linux-gnu
>>
>> locale:
>>  [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
>>  [5] LC_MONETARY=C              LC_MESSAGES=en_CA.UTF-8
>>  [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] splines   stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>>  [1] flowViz_1.9.9    lattice_0.17-26  flowStats_1.3.19 mvoutlier_1.4
>>  [5] fda_2.1.2        zoo_1.5-8        flowCore_1.11.22 rrcov_0.5-02
>>  [9] pcaPP_1.7        mvtnorm_0.9-7    robustbase_0.4-5 Biobase_2.5.8
>>
>> loaded via a namespace (and not attached):
>>  [1] feature_1.2.4      graph_1.23.7       grid_2.10.0
>> KernSmooth_2.23-3
>>  [5] ks_1.6.7           latticeExtra_0.6-1 MASS_7.3-2
>> RColorBrewer_1.0-2
>>  [9] stats4_2.10.0      tools_2.10.0
>>  >
>>
>> Am I just applying it in a stupid way or is there a bug?
>>
>> Thanks,
>> Josef
>>
>> --
>> 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
>> http://www.terryfoxlab.ca/people/rbrinkman/josef.aspx
>>
>>
>>
>>
>
> --
> Chao-Jen Wong
> 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
> 206.667.4485
> cwon2 at fhcrc.org
>
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