[BioC] flowStats's warping function problem

[Josef Spidlen]

Hi Chao-Jen,
> What I can do now is that I can
> wrap the fda package that I modified and email to you. What do you think?
That would be great,
thanks.

Josef

Chao-Jen Wong wrote:
> 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
>>
>>
>>
>>   
>>     
>
>   


-- 
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