[BioC] help with SPIA package

[Barbara Bo-Ju Shih]

Hi,
I am currently trying to use the SPIA bioconductor package and I came  
across an error that I am not sure how to solve it.

I used the contrast.fit method from Limma to obtain a list of  
significantly differentially expressed genes.
Following that, I wanted to use the SPIA package, but it kept on  
giving me the error :
"Error in spia(de = DE_top, all = ALL_top, organism = "hsa", nB = 2000,  :
    de must be a vector of log2 fold changes. The names of de should  
be included in the refference array!"

Would you know what the problem is? The fold change column from the  
contrast.fit method was not given as logFC, so I changed the names of  
the columns to FC. Would that be the issue?

I have attached the protocol I typed into Bioconductor at the end of  
this email.

Thank you very much for your help.

Regards
Barbara Bo Ju Shih


#### Limma ####
f<- factor (targets$GErep, levels=c("1", "2", "3")) reps<-c(1,2,3,4,3,  
5, 6,5,7,8,7,9, 10, 9, 11, 12, 13, 14, 15)  
arraycor<-duplicateCorrelation(exprs(esetPROC), block=reps)
design<-model.matrix(~0+f)
colnames(design)<-c("TopandMargin", "Middle", "Normal")

fit<-lmFit(exprs(esetPROC), design, cor=arraycor$consensus)

top_contrast.matrix<-makeContrasts(TopandMargin-Normal, levels=  
design) top_fit <-contrasts.fit (fit, top_contrast.matrix) top_fit <-  
eBayes(top_fit) top_TopTable<-topTable(top_fit, number=40000)

top<-top_TopTable

### SPIA ###
library(SPIA)
x <-hgug4112aENTREZID
top$ENTREZ <- unlist(as.list(x[top$ID])) top <- top[!is.na(top$ENTREZ), ]
tg1 <- top[top$adj.P.Val < 0.05, ]
DE_top = tg1$logFC
names(DE_top) <- as.vector(tg1$ENTREZ)
ALL_top = top$ENTREZ

DE_top[1:10]
ALL_top[1:10]

res = spia(de = DE_top, all = ALL_top, organism = "hsa",nB = 2000,  
plots = FALSE, beta = NULL)

-- 
Barbara Shih
Plastic and Reconstructive Surgery Research (PRSR)
Manchester Interdisciplinary Biocentre (MIB)
University of Manchester
131 Princess Street
Manchester. M1 7DN.
United Kingdom

University Lab            : 0044 161 306 8921
University Fax            : 0044 161 306 5177

Email                     : barbara.b.shih at manchester.ac.uk
Website                   : www.plasticsurgeryresearch.org