Question

Error in DEseq

0

Entering edit mode

Sanatan • 0

@5bdfba43

Last seen 2.4 years ago

India

I am trying to use a bulk RNA seq count matrix data to get DEGs using DESeq. The problem is mentioned below.

dds <- DESeqDataSetFromMatrix(countData=mycounts,colData=metadata,design=~dex, tidy=TRUE)

Error in `[.default`(countData, , 1) : incorrect number of dimensions

DEseq RNASeqData • 1.5k views

ADD COMMENT • link updated 2.5 years ago by ATpoint ★ 4.5k • written 2.5 years ago by Sanatan • 0

score 0 · Answer 1 · 2022-06-08

0

Entering edit mode

ATpoint ★ 4.5k

@atpoint-13662

Last seen 3 days ago

Germany

Please give some data examples. Probably metadata and mycounts do not match.

ADD COMMENT • link 2.5 years ago ATpoint ★ 4.5k

0

Entering edit mode

Here is the details

ADD REPLY • link 2.5 years ago Sanatan • 0

1

Entering edit mode

The Gene column must must be removed and relocated to rownames() of mycounts. The id column of metadata should also be the rownames of that object.

ADD REPLY • link 2.5 years ago ATpoint ★ 4.5k

0

Entering edit mode

Please find the details:

ADD REPLY • link 2.5 years ago Sanatan • 0

0

Entering edit mode

A data.frame with a character column (Gene) cannot be rounded. That's why I said remove the Gene column after assigning to rownames. Once done also remove the tidy argument.

ADD REPLY • link 2.5 years ago ATpoint ★ 4.5k