Question: EDASeq - Problem "longer object length is not a multiple of shorter object length"
0
gravatar for kaihami
4.3 years ago by
kaihami0
Brazil
kaihami0 wrote:

Hello,

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,

Regards

rna-seq edaseq • 3.6k views
ADD COMMENTlink modified 4.3 years ago by Ying W3.9k • written 4.3 years ago by kaihami0
0
gravatar for Ying W
4.3 years ago by
Ying W3.9k
South San Francisco, CA
Ying W3.9k wrote:

For future bioconductor related questions, you might get a quicker response here: https://support.bioconductor.org/

There is mismatch in dimensions when running newSeqExpressionSet()

Try assigning it separately not within the function:

pd = data.frame(samples)
rowNames(pd) = colNames(x)
set <- newSeqExpressionSet(x, pd)

Also, make sure the names are unique (ctrl1 ctrl2 ctrl3 not just ctrl)

ADD COMMENTlink written 4.3 years ago by Ying W3.9k
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