DESeq2
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Cosmic • 0
@4f41ba09
Last seen 4 days ago
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Hi. I have two RNa seq datasets generated from same cell line at different time for same treatment of drugs. First dataset is vehicle only vs Treated with drug for 2 days , and another dataset in same cell line where vehicle only and 6 day drug treatment. If both these data sets are generated separately from sample prep to analysis. Now I feel I should have done at same time to get idea what are effect of drug at day 2 vs day 6. Can I reanalyze my both data sets together in DESeq2 ? I am thinking this is possible making use of batch effect and design formulae in DESeq2 ?
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData • 479 views
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ATpoint ★ 4.8k
@atpoint-13662
Last seen 1 day ago
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Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then its confounded and you cannot do anything about it.
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