Error in DEseq
1
0
Entering edit mode
Sanatan • 0
@5bdfba43
Last seen 3 months 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 • 260 views
ADD COMMENT
0
Entering edit mode
ATpoint ★ 1.6k
@atpoint-13662
Last seen 13 hours ago
Germany

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

ADD COMMENT
0
Entering edit mode

Here is the details

ADD REPLY
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
0
Entering edit mode

Please find the details:

ADD REPLY
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

Login before adding your answer.

Traffic: 501 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6