Originally posted by Anomilie
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The double quote is directly copied from the documentation and is apparently requirement for subsetting the DGEList object.
the following code sorted out that issue (in case someone else has similar problems)
Code:dge <- DGEList(counts=raw_data, genes=geneID)
Thanks for your reply Cytosine
While on the topic of diffSplice, would you know the statistical difference between using that function and performing the DE with the standard limma voom pipeline using eBayes(fit)?Last edited by Anomilie; 08-04-2014, 11:42 PM.
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Please provide sessionInfo() so we can better assist you...
Code:dge <- dge[A>10[COLOR="Red"],,[/COLOR]keep.lib.sizes=FALSE] Error in object[[a]][i, , drop = FALSE] : incorrect number of dimensions
Code:Error: could not find function "diffSplice"
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Limma Voom Differential Splicing diffSplice() error
Hi,
I've been following the user's guide for Limma voom to perform differential splicing analysis and I have encountered a few problems.
Firstly, In chapter 15.4 the following line of code produces and error:
Code:dge <- dge[A>10,,keep.lib.sizes=FALSE] Error in object[[a]][i, , drop = FALSE] : incorrect number of dimensions
Code:isexpr <- rowSums(dge$counts) > 10 x <- x[isexpr,] dge <- calcNormFactors(x)
Code:v <- voom(dge,design,plot=TRUE) fit <- lmFit(v, design) ex <- diffSplice(fit, geneid="GeneID") Error: could not find function "diffSplice"
Thanks in advanceLast edited by Anomilie; 08-04-2014, 08:17 PM.
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