plotting Signalling Pathways using SPIA
Entering edit mode
Assa Yeroslaviz ★ 1.5k
Last seen 5 weeks ago

I'm using the SPIA package to infer and plot signaling pathways. All works fine, but I get a strange error when plotting the sig. pathways using the plotP command.

This is my code

spia_result <- spia(de=sig_entrez, all=background_entrez, organism="hsa")
head(spia_result, n=5)
plotP(spia_result, threshold=0.1)

whereas the two vectors are of entrez genes. It all works and I also get the table of sig. patways. But when I plot the evidence plot I get this error:

Error in if (sum(oky) > 0) { : missing value where TRUE/FALSE needed

Is this because of my NA values in the column pPERT? The plot is created, so I would just like to know if this is aa problem or if I can ignore it?


SPIA functional-analysis Pathways KEGG • 254 views

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