[BioC] a question on SPIA package

[Alex Gutteridge]

 On Mon, 22 Aug 2011 07:56:28 -0700, Jing Huang wrote:
> Dear Adi and other members,
>
> I am trying to apply my microarray data to SPIA R package that is
> created by Adi Tarca. I only got one pathway. I am wondering if I did
> anything wrong. Could you help me on this?
>
> I attached my topTable of fit data that contains lists of genes that
> is differently expressed, LFC , p.value, adj.p.value and so on.

 [...]

>> library(SPIA)
>> x=topTable(fit,coef="HIF1a")

 topTable only returns the top 10 genes by default so it looks to me 
 like your gene universe only contains 10 genes. Check the length of 
 HIF1a1 to be sure. If that is the case then

 x=topTable(fit,coef="HIF1a",number=Inf)

 Should do something closer to what you want.

>> library(hgu133plus2.db)
> Loading required package: AnnotationDbi
> Loading required package: org.Hs.eg.db
> Loading required package: DBI
>
>
>> y=hgu133plus2ENTREZID
>> x$ENTREZ=unlist(as.list(y[x$ID]))
>> x=x[!is.na(x$ENTREZ),]
>> x=x[!duplicated(x$ENTREZ),]
>> tg1=x[x$adj.P.Val<0.1,]
>> HIF1a=tg1$logFC
>> names(HIF1a)=as.vector(tg1$ENTREZ)
>> HIF1a1=x$ENTREZ
>> 
>> res=spia(de=HIF1a,all=HIF1a1,organism="hsa",nB=2000,plots=F,beta=NULL,combine="fisher",verbose=F)
>> res
>            Name    ID pSize NDE pNDE tA pPERT pG pGFdr pGFWER    
> Status
> 1 RNA transport 03013     1   1    1  0    NA  1     1      1 
> Inhibited
>                                                     KEGGLINK
> 1 http://www.genome.jp/dbget-bin/show_pathway?hsa03013+54913
>
>
> Many Many Thanks
>
> Jing Huang PhD
>
> Oregon Health $ Sciences University
>
> Portland Oregon

-- 
 Alex Gutteridge