I'm having a really bad time with R, indeed I'm really new in R programming...
I'm trying to analyse some RNA-Seq data, I have 10 samples (5 controls, 5 treatment).
I have loaded the raw count (the file is separated as the first column gene name, the following columns samples).
Therefore I have a table with (n rows and 10 columns).
I transformed it in a matrix [ x <- as.matrix(table)].
And created an object called samples:
samples <- as.factor(c(rep("Control", 5), rep("Treatment", 5))
And then used EDASeq package
set <- newSeqExpressionSet(x, # the matrix "x" created before
phenoData <- data.frame(samples, row.names <- colnames(x))
It should work, but I got a Error message
Error in assayDataNew(counts = counts, normalizedCounts = normalizedCounts, :
'AssayData' elements with different rowNames
In addition: Warning message:
In eltRowNames == rownames(assayData[[elt]]) :
longer object length is not a multiple of shorter object length
Anybody can really help me? If I am not wrong, I should get this kind of error if the colnames in x is different of the phenoData rownames. But since I used row.names <-colnames(x) it should work but It is not the case =/
I'll appreciate any help,