Question

DEseq2 sample imbalance

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aishu.jp ▴ 30

@aishujp-15144

Last seen 4.4 years 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 • 1.2k views

ADD COMMENT • link 6.9 years ago aishu.jp ▴ 30

score 0 · Answer 1 · 2018-03-02

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Michael Love 43k

@mikelove

Last seen 1 day 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 • link 6.9 years ago Michael Love 43k

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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