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(mgu74av2ENTREZI D)[, 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=N ULL,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 [[alternative HTML version deleted]]

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$ENTREZ >>head(WThypo) >[1] "11535" "20525" "11839" "15277" "11910" "18639" However, that seems to be the problem. In the error message is clearly says that you need "a vector of log2 fold changes", not a character vector. Best, --Johannes -----Original Message----- From: Jing Huang [mailto:huangji@ohsu.edu] Sent: Wednesday, August 24, 2011 1:22 PM To: 'bioconductor at r-project.org' Subject: [BioC] question on SPIA pavkage application Thank You so much for all of you. I tried and it works on previous problem. Now I am having another problem. I am so sorry for not being able to solve problems myself. Can somebody advise me? Here is the R to follow SPIA package: >x=topTable(fit,coef=WThypo,n==1003) >library(mgu74av2.db) >y=mgu74av2ENTREZID >x$ENTREZ=toTable(mgu74av2ENTREZID)[match(x$ID,toTable(mgu74av2ENTREZI D)[, 1]), 2] >x=x[!is.na(x$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=N ULL,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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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(mgu74av2ENTREZ ID)[, >> 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