Handling RNA-seq samples from the same individual in DEseq2 analysis
1
0
Entering edit mode
3.3 years ago
gspirito ▴ 10

Hello everyone, here's my question:

I have a dataset of RNA-seq data, where I have gene counts of different tissues from the same individuals in two conditions, like so:

enter image description here

In order to perform a differential expression analysis with DEseq2, comparing KO vs. WT of both tissues together, would it be correct to use this design?:

ddsFullCountTable <- DESeqDataSetFromMatrix(countData = counts.txt, colData = metadata.txt, design = ~Individual+Group, tidy=TRUE)

Thank you in advance

DEseq2 RNA-seq • 599 views
ADD COMMENT
2
Entering edit mode
3.3 years ago

Yes, that'd be the appropriate design if you want to account for differences between the individuals.

ADD COMMENT

Login before adding your answer.

Traffic: 1730 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