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


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,


rna-seq edaseq • 4.0k views
ADD COMMENTlink modified 5.2 years ago by Ying W4.0k • written 5.2 years ago by kaihami0
gravatar for Ying W
5.2 years ago by
Ying W4.0k
South San Francisco, CA
Ying W4.0k wrote:

For future bioconductor related questions, you might get a quicker response here:

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 5.2 years ago by Ying W4.0k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1186 users visited in the last hour