DEseq2 sample imbalance
1
1
Entering edit mode
aishu.jp ▴ 20
@aishujp-15144
Last seen 12 months ago
I have a RNA seq data which I am trying to identify DEGs. Dataset contains Untreated - 2 replicates (time point 0hr) Treated - 4 replicates (2 replicates at 6hr and 2 replicates at 12 hr) I merged all the samples and tried to identify DEGs untreated vs treated. Is it correct to merge all samples and compare. Or should I compare the two time point treated samples with untreated as 0hr vs 6hr and 0hr vs 12hr.
deseq • 587 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 2 hours ago
United States

I'd recommend a LRT where you find any changes at any time point. See the vignette on the LRT. You would use a reduced design of ~1 (no changes over time).

ADD COMMENT
0
Entering edit mode

After doing the LRT test, to identify the significant genes the cutoff used was adjP<0.05.  Approximately 10000 genes were obtained after cutoff. Can you use rlog transformation as normalization on these 10000 genes for gene co-expression network construction. Does doing LRT test will make any change in construction of a co-expression network

ADD REPLY
0
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 286 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