[BioC] SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive.

[Tarca, Adi]

Hi Ilario,

The error: " density.default(pfstmp, bw = sd(pfstmp)/4) :  \'bw\' is not positive." occurs when a pathway gets only few DE genes (e.g. 1 or 2) and the pathway in question has only few connections so that the resulting standard deviation of the empirical perturbation accumulations (sd(pfstmp)) is 0. 
The work around is to turn the argument plots=F since those plots are optional. Alternatively, you can use the pathids argument to specify which pathways you want to analyze, in this case all but pathway 20. The ids of all pathways analyzed by SPIA for mmu organism can be found using:    

load(system.file("extdata/mmuSPIA.RData",package="SPIA"))
x=names(path.info)

The pathway that cause the problem is in this case
unlist(lapply(path.info,function(x){x$title}))[20]
     04142
"Lysosome"

So setting pathids=setdiff(x,c("04142")) should avoid the error.

The third option would be to modify the spia function itself and change the line:
if (plots) {

to 

if (plots&& sd(pfstmp)!=0) {


I will fix this in the next release.


Adi



Adi Laurentiu TARCA, Ph.D. 
Assistant Professor (Research),
Department of Computer Science & Center for Molecular Medicine and Genetics, Wayne State University,
Director, Bioinformatics and Computational Biology Unit,  Perinatology Research Branch (NICHD),
3990 John R., Office 4809,
Detroit, Michigan 48201
Tel: 1-313-5775305

-----Original Message-----
From: Ilario De Toma [guest] [mailto:guest at bioconductor.org] 
Sent: Wednesday, December 11, 2013 3:55 AM
To: bioconductor at r-project.org; detoma.ilario at hsr.it
Cc: Tarca, Adi
Subject: SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive.


Hi everyone,

I encounter the following error after having successful started my analysis with the SPIA package.

res1.5=spia(summarized1.5, all, organism="mmu", plots=T)

Done pathway 1 : RNA transport..
Done pathway 2 : RNA degradation..
Done pathway 3 : PPAR signaling pathway..
Done pathway 4 : Fanconi anemia pathway..
Done pathway 5 : MAPK signaling pathway..
Done pathway 6 : ErbB signaling pathway..
Done pathway 7 : Calcium signaling pathway..
Done pathway 8 : Cytokine-cytokine receptor int..
Done pathway 9 : Chemokine signaling pathway..
Done pathway 10 : NF-kappa B signaling pathway..
Done pathway 11 : Phosphatidylinositol signaling..
Done pathway 12 : Neuroactive ligand-receptor in..
Done pathway 13 : Cell cycle..
Done pathway 14 : Oocyte meiosis..
Done pathway 15 : p53 signaling pathway..
Done pathway 16 : Sulfur relay system..
Done pathway 17 : SNARE interactions in vesicula..
Done pathway 18 : Regulation of autophagy..
Done pathway 19 : Protein processing in endoplas..Error in density.default(pfstmp, bw = sd(pfstmp)/4) : 
  'bw' is not positive.

I thank you in advance for you answer,

Ilario De Toma


 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pathview_0.99.10     org.Hs.eg.db_2.8.0   RSQLite_0.11.2       DBI_0.2-5           
 [5] AnnotationDbi_1.20.7 Biobase_2.18.0       BiocGenerics_0.4.0   KEGGgraph_1.14.0    
 [9] graph_1.34.0         XML_3.95-0.1         SPIA_2.8.0           BiocInstaller_1.8.3 

loaded via a namespace (and not attached):
[1] grid_2.15.3     IRanges_1.16.6  parallel_2.15.3 png_0.1-4       Rgraphviz_2.2.1
[6] stats4_2.15.3   tools_2.15.3  

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