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Question: DEseq2 sample imbalance
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gravatar for aishu.jp
4 months ago by
aishu.jp10
aishu.jp10 wrote:
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.
ADD COMMENTlink modified 3 months ago • written 4 months ago by aishu.jp10
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gravatar for Michael Love
4 months ago by
Michael Love18k
United States
Michael Love18k wrote:

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 COMMENTlink written 4 months ago by Michael Love18k

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 REPLYlink written 4 months ago by aishu.jp10

Looks like this was answered here:

A: DESeq LRT test and construction of Co-expression network

ADD REPLYlink written 3 months ago by Michael Love18k
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