[BioC] question on SPIA pavkage application

[Alex Gutteridge]

 On Wed, 24 Aug 2011 10:22:10 -0700, Jing Huang wrote:
> Thank You so much for all of you.
>
> I tried and it works on previous problem.
>
> Now I am having another problem. I am so sorry for not being able to
> solve problems myself. Can somebody advise me?
>
> Here is the R to follow SPIA package:
>
>>x=topTable(fit,coef=WThypo,n==1003)
>>library(mgu74av2.db)
>>y=mgu74av2ENTREZID
>>x$ENTREZ=toTable(mgu74av2ENTREZID)[match(x$ID,toTable(mgu74av2ENTREZID)[, 
>> 1]), 2]
>>x=x[!is.na(x$ENTREZ),]
>>x=x[!duplicated(x$ENTREZ),]
>>tg1=x[x$adj.P.Val<0.1,]
>>WThypo=tg1$logFC
>>head(WThypo)
>
> [1]  4.80  3.27  2.65  2.63  3.03 -3.41
>
> At this step: I should received a outcome like this:
>
>      11535  20525   11839  15277   11910    18639
>
> [1]  4.80   3.27    2.65    2.63    3.03    -3.41
>
>>WThypo1=x$ENTREZ
>>head(WThypo)
>
> [1] "11535" "20525" "11839" "15277" "11910" "18639"
>
>>res=spia(de=WThypo,all=HWThypo1,organism="mmu",nB=2000,plots=F,beta=NULL,combine="fisher",verbose=F)
>
> Error in spia(de = WThypo, all = WThypo1, organism = "mmu", nB = 
> 2000,  :
>
>   de must be a vector of log2 fold changes. The names of de should be
> included in the refference array!
>
> I am not sure what I did wrong. I didn't have issue with this
> procedure before.

 Last time you correctly set the names of the DE gene vector to be the 
 Entrez IDs. So you need:

 names(WThypo) = tg1$ENTREZ

 before running spia.

-- 
 Alex Gutteridge