[BioC] poe.mcmc - metaArra non-numeric matrix extent error

Adrian Johnson oriolebaltimore at gmail.com
Sun Oct 21 14:12:27 CEST 2012


I am trying to replicate the code in metaArray package.

The merged object after mergeExprs does not seem to work for poe.mcmc.
Could anyone help me understand where the problem exist. Thanks in advance.

> poe.mat <- poe.mcmc(merged,M=1000)
Error in matrix(0, GG, TT) : non-numeric matrix extent

I am using merged object from mergeExprs function from mergeMaid.
Following is the code I used. This code is chunk1 from metaArray
vignette ( october 1 2012)


## code chunk 1 ### from metaArray vignette
common <- intersect(rownames(chen.poe),rownames(garber.poe))
common <- intersect(common, rownames(lapointe.poe))
chen.poe <- chen.poe[match(common, rownames(chen.poe)),]
garber.poe <- garber.poe[match(common, rownames(garber.poe)),]
lapointe.poe <- lapointe.poe[match(common, rownames(lapointe.poe)),]
vars <- list("var1","var2")
names(vars) <- names(chen.spl)
pdata1 <- new("AnnotatedDataFrame")
pData(pdata1) <- chen.spl
varLabels(pdata1) <- vars
sample1 <- new("ExpressionSet", exprs=chen.poe, phenoData = pdata1)
names(vars) <- names(garber.spl)
pdata2 <- new("AnnotatedDataFrame")
pData(pdata2) <- garber.spl
varLabels(pdata2) <- vars
sample2 <- new("ExpressionSet", exprs=garber.poe, phenoData = pdata2)
names(vars) <- names(lapointe.spl)
pdata3 <- new("AnnotatedDataFrame")
pData(pdata3) <- lapointe.spl
varLabels(pdata3) <- vars
sample3 <- new("ExpressionSet", exprs=lapointe.poe, phenoData = pdata3)
merged <- mergeExprs(sample1,sample2,sample3)

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