DESeq2 Error Fix: DESeqDataSetFromMatrix ncol(countData) == nrow(colData) is not TRUE
In this video I address following common errors encountered to create DESeqDataSetFromMatrix using counts matrix and colData (i.e. sample metadata).
• Error in DESeqDataSetFromMatrix(countData = countData, colData = colData, : ncol(countData) == nrow(colData) is not TRUE
• all(colnames(counts_data) == rownames(colData)) is not TRUE
I talk about what these errors mean, why we get these errors and demonstrate how to fix these errors. I hope you find this video helpful! Leave your thoughts in the comment section below!
Link to Code:
DESeq2 Error fix: https://github.com/kpatel427/YouTubeT...
DESeq2 workflow script: https://github.com/kpatel427/YouTubeT...
Chapters:
0:00 Intro
1:28 Condition 1: nrow(colData) == ncol(counts_data)
3:27 Condition 2: all(rownames(colData) %in% colnames(counts_data))
5:13 Condition 3: all(colnames(counts_data) == rownames(colData))
7:17 Demo: How to check data for all 3 conditions?
9:52 Demo: How to get column names in counts_data to be in same order as row names in colData?
You can show your support and encouragement by buying me a coffee:
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To get in touch:
Website: https://bioinformagician.org/
Github: https://github.com/kpatel427
Email: [email protected]
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