[BioC] SPIA package

[Jing Huang]

Dear Adi and all members,

I am following instructions of SPIA package and trying to predict pathways for Arabidopsis thaliana (ath). I did not get any output.  Hope somebody take a look and advise me.

Here is the R:

>library(SPIA)
> x=x[!is.na(x$ENTREZ_GENE_ID),]
> x=x[!duplicated(x$ENTREZ_GENE_ID),]
> tg1=x[x$adj.P.Val<0.1,]
> Hypo2h=tg1$logFC
> names(Hypo2h)=as.vector(tg1$ENTREZ_GENE_ID)
> Hypo2h1=x$ENTREZ_GENE_ID
> head(Hypo2h)
           821893            821112            826619            823393 817537 /// 818002            822341
         5.515566          5.230701          5.222565          5.197203          6.310680          4.918854
> length(Hypo2h)
[1] 4995
> head(Hypo2h1)
[1] 821893            821112            826619            823393            817537 /// 818002 822341
21218 Levels:  3767970 /// 3768186 6240645 815346 815347 815383 815412 815417 817196 817198 817199 817203 ... 817844
> length(Hypo2h1)
[1] 4995
> res=spia(de=Hypo2h,all=Hypo2h1,organism="ath",nB=2000,plots=F,beta=NULL,combine="fisher",verbose=F)
> dim(res)
[1]  0 12

Arabidopsis thaliana Rdatabase (athSPIA.RData) is downloaded and stored at :

C:\Program Files\R\R-2.13.1\library\SPIA\extdata\

Many thanks

Jing