[BioC] question on SPIA pavkage application

[Freudenberg, Johannes (NIH/NIEHS) [E]]

Hi Jing,

I'm not sure how you got from here:

>>head(WThypo)
>[1]  4.80  3.27  2.65  2.63  3.03 -3.41

which look like log2 fold changes to me, to here, a character vector:

>>WThypo1=x$ENTREZ
>>head(WThypo)
>[1] "11535" "20525" "11839" "15277" "11910" "18639"

However, that seems to be the problem.  In the error message is clearly says that you need "a vector of log2 fold changes", not a character vector.  

Best,
--Johannes


-----Original Message-----
From: Jing Huang [mailto:huangji at ohsu.edu] 
Sent: Wednesday, August 24, 2011 1:22 PM
To: 'bioconductor at r-project.org'
Subject: [BioC] question on SPIA pavkage application

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.


Many Many Thanks

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