Question: SPIA plotP giving error
0
gravatar for docpriya21
2.9 years ago by
docpriya210
docpriya210 wrote:

Hello

I'm using SPIA on my toptable generated by limma. I have R version 3.3.1, and updated biocLite to the latest version. It makes the results file using 

res=spia(de=DE,all=ALL,organism="hsa",nB=2000,plots=FALSE,beta=NULL,combine="fisher")

However, when I use

plotP(res,threshold=0.05)

I get the following error message, and it doesn't plot. 

Error in plotP(res, threshold = 0.05) : 
  The threshold value should be 0.173107798207408 or higher!!!

It plots when I use 0.1732 for threshold but no points fall to the right of the oblique line. I'm not sure what else to do. 

Here is the output of sessionInfo():=

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.1 (Sierra)

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] SPIA_2.26.0          KEGGgraph_1.32.0     BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] parallel_3.3.1      tools_3.3.1         BiocGenerics_0.20.0
[4] stats4_3.3.1        XML_3.98-1.5        graph_1.52.0       

 

Thanks

Priya

spia plotp threshold • 415 views
ADD COMMENTlink written 2.9 years ago by docpriya210

I have the same problem/question. Looking at the code: https://rdrr.io/bioc/SPIA/src/R/plotP.R

if(threshold<x[1,"pgfdr"]){ msg&lt;-paste("the="" threshold="" value="" should="" be",x[1,"pgfdr"],"or="" higher!!!");="" stop(msg);="" }<="" p="">

Then at the explanation: https://www.rdocumentation.org/packages/SPIA/versions/2.24.0/topics/spia

"pGFdr and pGFWER are the False Discovery Rate and respectively Bonferroni adjusted global p-values."

So...

ADD REPLYlink written 9 months ago by maxininfa0
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