Dear Adi, dear list,

I am trying to run SPIA on some data generated using limma. I am, however,
running into an error message I don´t understand - my data (at least to me)
look very similar to the "Colorectal" example data set used in the vignette.

For the ALL list, I did the following. As ALL_Colorectal, all is a
character vector of Entrez IDs.

> entrezid = mget(ids, illuminaMousev2ENTREZID, ifnotfound = NA)

> all <- as.vector(as.numeric(entrezid))

> all <- na.omit(all) > all <- as.character(all)


> is.vector(all)[1] TRUE

> length(all)[1] 20573

> all[1][1] "66836"


> is.vector(ALL_Colorectal)[1] TRUE> length(ALL_Colorectal)[1] 18045

> data(colorectalcancer)

> ALL_Colorectal[1][1] "3491"


For the DE list, I did.

> pg=topTable(ebFit, coef=1, number=1000, p.value=0.05, lfc=1)

> de_pg <- pg[,5]> names(de_pg)<-pg[,3]


de_pg is a numerical vector of log2 fold changes, with EntrezIDs as names,
as DE_Colorectal, the example dataset.

> is.vector(de_pg)[1] TRUE

> de_pg[1]   14825
5.189596


> is.vector(DE_Colorectal)[1] TRUE> DE_Colorectal[1]    3491
5.960206



The names of de_pg are in all, similar to the names of DE_Colorectal
being in ALL_Colorectal


> names(de_pg) %in% all  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE etc ...

> names(DE_Colorectal) %in% ALL_Colorectal   [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE etc ...



However, when I run spia, I get an error I cannot understand


> res<-spia(de=de_pg, all=all, organism="mmu",beta=NULL,nB=2000,plots=FALSE, verbose=TRUE,combine="fisher")


Error in spia(de = de_pg, all = all, organism = "mmu", beta = NULL, nB
= 2000,  :
  de must be a vector of log2 fold changes. The names of de should be
included in the refference array!




What am I doing wrong?



Many thanks for your help,





Moritz

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