Question: Issue with DESeq2: Unable to create a DESeqDataSet because names in colData don't match column names in countData
gravatar for catglen012
15 months ago by
catglen0120 wrote:

Hello! I loaded my gene(/transcript) count matrix and labels into DESeq2:

> countData <- as.matrix(read.csv(file.choose(), row.names = "gene_id"))
> colData <- read.table(text = readLines(file.choose(), warn = FALSE), header = TRUE, sep = "," )

But when I check that all sample IDs in colData are also in CountData and match their orders, I obtain the following:

> all(rownames(colData) %in% colnames(countData))

It then checked to see how my gene_count_matrix.csv looks like and the column has MSTRG as the gene ID and it does not match the ID names found in phenotype_data.

I was wondering how do I make them both match so that I am able to generate a DESeqDataSet? My phenotype_data looks just like the data found in the nature paper

and I followed exactly the protocol for Using StringTie with DESeq2.

rna-seq deseq2 R • 731 views
ADD COMMENTlink written 15 months ago by catglen0120

Please post the first line of countData and the contents of colData.

ADD REPLYlink written 15 months ago by Devon Ryan92k


gene_id    Ceratodon_GG1    Ceratodon_R40
MSTRG.9134      3497                  998


ids                 sex
Ceratodon_GG1   female
ADD REPLYlink written 15 months ago by catglen0120

You only have 2 samples?

ADD REPLYlink written 15 months ago by Devon Ryan92k

hello! I was able to resolve the issue by fixing how the colData is arranged. Thanks for the help nevertheless.

ADD REPLYlink written 14 months ago by catglen0120
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: 709 users visited in the last hour