How to remove batch effect from multiple rna-seq dataset before running deseq2
1
0
Entering edit mode
Yosapol • 0
@40f341c9
Last seen 12 days ago
Netherlands

Dear all,

I would like to compare three RNA-seq datasets of early plants, young plants, and old plants. These three datasets were prepared in different time points and techniques.

My question is how gene A changes over developmental time. Would it be possible to combine these three available data for analysis? How do you remove the batch effect before running Deseq2?

Thank you very much for sharing. Best regards, Yosapol

DESeq2 • 130 views
ADD COMMENT
2
Entering edit mode
swbarnes2 ▴ 780
@swbarnes2-14086
Last seen 8 hours ago
San Diego

RNAseq is very sensitive to batch effect. If developmental stage and technical batch are totally confounded, there is no valid way to look at the data together. Any and every difference you see could 0% biological, and 100% caused by technical differences.

ADD COMMENT
0
Entering edit mode

Thank you very much for replying swbarnes2

ADD REPLY

Login before adding your answer.

Traffic: 290 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