[BioC] flowStats's warping function problem

[Chao-Jen Wong]

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