Dear All members,
I am using SPIA package to incorporate the pathway information that
related to differentially expressed the genes. However, some organisms
such as Drosophila are not included in the package. I downloaded the
data but not sure how to incorporate the data to R and process. Can
somebody help me ?
I have downloaded the data:
load("/Users/huangji/Downloads/dmeSPIA.RData")
Here is the R scripts for predicting the pathways:
res=spia(de=CH,all=CH1,organism="dme",nB=2000,plots=F,beta=NULL,combin
e="fisher",verbose=F)
Many THANKS
Jing
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Dear Adi and all members,
I am following instructions of SPIA package and trying to predict
pathways for Arabidopsis thaliana (ath). I am not sure why it didn't
have 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=N
ULL,combine="fisher",verbose=F)
> dim(res)
[1] 0 12
Arabidopsis thaliana R.database (athSPIA.RData) is downloaded and
stored at :
C:\Program Files\R\R-2.13.1\library\SPIA\extdata\
Many thanks
Jing
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