Trying to combine two different datasets by MergeMaid

Question

[Macy W]

Hello guys,

I am trying to combine two microarray datasets downloaded from GEO, they were produced from different platforms. I used poe ( command is poe.mcmc, it is a function of metaArray) to transform their expression value separately and then merged them by using MergeMaid. Before I merged, I changed their row names from probe id to Gene bank accession number. But after I merged, there is no any expression value in the merged file (I used summary(merged) to check). Please please please help me with this problem.

The command line I used is below (follow the description from metaArray vignette):

common <-intersect(rownames(exprs(gse1)),rownames(exprs(gse2)))
set1<-exprs(gse1)
set2<-exprs(gse2)
set1 <- set1[match(common, rownames(set1)),]
set2 <- set2[match(common, rownames(set2)),]
varsubset1<-subset(pData(gse1),select=c(description,title))
varsubset2<-subset(pData(gse2),select=c(description,title))
vars<-list("var1","var2")
names(vars) <- names(varsubset1)
names(vars)
pdata1 <- new("AnnotatedDataFrame")
pData(pdata1) <- varsubset1
varLabels(pdata1) <- vars
sample1 <- new("ExpressionSet", exprs=set1, phenoData = pdata1)
names(vars)<-names(varsubset2)
pdata2 <- new("AnnotatedDataFrame")
varLabels(pdata2) <- vars
pData(pdata2) <- varsubset2
varLabels(pdata2) <- vars
sample2 <-new("ExpressionSet", exprs=set2, phenoData = pdata2)
merged <- mergeExprs(sample1,sample2)

---

first few lines of set1 is this format :

                GSM1            GSM2         GSM3
NM_005505       -0.14284213     0.006953089  0.38606952 ...
NM_015140       -0.19068979     0.273505839  0.24988608 ...

Much appreciate,
Macy

[Manvendra Singh]

what if instead of

common <-intersect(rownames(exprs(gse1)),rownames(exprs(gse2)))

u use

A1=exprs(gse1)
A2=exprs(gse2)
common = merge(A1, A2, by="row.names", all=FALSE)

see if it comes otherwise, we would start modifying other commands.