Question: diffSplice: Error in exon.genes[o, , drop = FALSE] : incorrect number of dimensions
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gravatar for sarin.heikki.v
20 months ago by
sarin.heikki.v10 wrote:

I'm trying to run the exon level analysis RNA-seq data according to: https://www.bioconductor.org/help/course-materials/2014/BioC2014/BioC2014_edgeR_voom.html#/38. . However for some reason after running the diffSplice it gives me the error: Error in exon.genes[o, , drop = FALSE] : incorrect number of dimensions. No idea where that might come from. Both geneid and exonid vectors are character vectors as they are supposed to be. Could anyone help with this. The code is shown below:

dge <- DGEList(counts=countdata_merged, samples = coldata, group = coldata$CASE_CONTROL)
dge$genes$GeneID <- GeneID

#Lets do the model matrix

x <- model.matrix(~ CASE_CONTROL + PRE_MID_POST + CASE_CONTROL:subject.nested + CASE_CONTROL:PRE_MID_POST, coldata)
all.zero <- apply(x, 2, function(x) all(x==0))
all.zero

idx <- which(all.zero)
full <- x[,-idx]
design <- full
design
#Lets do some prefiltering if we want to
A <- rowSums(dge$counts)
dge <- dge[A>10, ,keep.lib.sizes=FALSE]

#Lets calculate the calcNormFactors
dge <- calcNormFactors(dge)

#Linear modelling
v <- voom(dge,design,plot=TRUE)
fit <- lmFit(v,design)

# 1)  DiffSplice
ex <- diffSplice(fit, geneid= "GeneID", exonid = "ExonID", verbose=TRUE)

Error in exon.genes[o, , drop = FALSE] : incorrect number of dimensions

voom edger diffsplice exon • 820 views
ADD COMMENTlink modified 20 months ago by WouterDeCoster38k • written 20 months ago by sarin.heikki.v10

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ADD REPLYlink written 20 months ago by WouterDeCoster38k
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