Issue with DESeq2: Unable to create a DESeqDataSet because names in colData don't match column names in countData

Question

[catglen012]

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))
[1] FALSE

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

https://www.nature.com/articles/nprot.2016.095

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

[Devon Ryan]

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

[catglen012]

countData:

gene_id    Ceratodon_GG1    Ceratodon_R40
MSTRG.9134      3497                  998

colData:

ids                 sex
Ceratodon_GG1   female

[Devon Ryan]

You only have 2 samples?

[catglen012]

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

[c_u]

Hi catglen012, could you mention what exactly you did to the colData to fix it? I have the same issue