User: hdf87ery

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Posts by hdf87ery

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Comment: C: Question about statistical model and experiment design in DEseq2
... Hi Michael, Thank you for your reply. According to this thread https://support.bioconductor.org/p/62355/#62442 There are "if a gene is DE in W and M, but a different size of difference: (1), (2), (3)" "if a gene is DE in W and M, and the same size of difference: (2) and (3)" So, no matter I want ...
written 3.6 years ago by hdf87ery0
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Answer: A: Question about statistical model and experiment design in DEseq2
... Hi, I like to test genes that upregulated in both KDvsGFPinTotal and KDvsGFPinNascent. In other words, I want to test genes that have the same size of difference. According to this thread https://support.bioconductor.org/p/62355/#62442, "(1) interaction term, (2) treatment effect in W, (3) treatme ...
written 3.6 years ago by hdf87ery0
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Answer: A: Question about statistical model and experiment design in DEseq2
... Hi  Michael, Thank you for your reply. I still have some questions about statistical model. The equation (KDvsGFPinNascent)/(KDvsGFPinTotal) is equal to ("groupkdnascent"/"groupgfpnascent")/ ("groupkdtotal"/"groupgfptotal") [E1] , but it can only be divided one time in DEseq2, so my work around i ...
written 3.6 years ago by hdf87ery0
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Question about statistical model and experiment design in DEseq2
... Hi, I like to confirm if the statistical model of Deseq2 is appropriate for my experiment design. Here’s my code. > dds<-DESeqDataSetFromMatrix(countData=countsTable,colData,formula(~ Transfection*Enrichment )) > colData(dds)$Transfection<-factor(colData(dds)$Transfection,levels=c("gfp ...
deseq2 statistical learning written 3.6 years ago by hdf87ery0

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