User: lihongfei93

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Posts by lihongfei93

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Comment: C: DEseq2: Why low counts mean count < 804
... Thanks for your reply. I got 439 DEGs by subset res with padj < 0.05 when I didn't turn off independent filtering. But why I got 348 DEGs when I turn it off? shouldn't it be more DEGs when I turn off independent filtering? ...
written 5 months ago by lihongfei930
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DEseq2: Why low counts mean count < 804
... Hi, When launching the DESeq function, I get results like this: res<- results(dds, name="genotypeA.treatment2") > summary(res) out of 20717 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 154, 0.74% LFC < 0 (down) : 7, 0.034% outliers [1] : 5, 0.0 ...
deseq2 written 5 months ago by lihongfei930 • updated 5 months ago by Michael Love24k
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Comment: C: Usage of interactions for multi-factor analysis
... Thanks for your reply. I am not sure if I understand correctly. So if aiming to answer treatment effect (e.g ABA treatment) between(not separately) genotype ds2.3 and reference genotype, using results(dds, name="genotypeds2.3.treatmentABA") is the right way. For treatment effect in a non-referenc ...
written 5 months ago by lihongfei930
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Comment: C: DEseq2: Usage of interactions for multi-factor analysis
... Sorry for the confusing. The previous one has a bad typesetting which makes my question unclear, so could you please reopen this one and close the previous one? Thanks a lot! ...
written 5 months ago by lihongfei930
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(Closed) DEseq2: Usage of interactions for multi-factor analysis
... Hello, I am working on RNASEQ data with 4 treatments(Control, ABA, salt,sorbitol), 3 genotypes(col.0, lbd16-1, ds2.3) and three replicates. To test differently expressed genes of treated/untreated effect between lbd16 and col.0, I wrote my script like this: dds <- DESeqDataSetFromMatrix(countda ...
deseq2 written 5 months ago by lihongfei930
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Usage of interactions for multi-factor analysis
... Hello, I am working on RNASEQ data with 4 treatments(Control, ABA, salt,sorbitol), 3 genotypes(col.0, lbd16-1, ds2.3) and three replicates. To test differently expressed genes of treated/untreated effect between lbd16 and col.0, I wrote my script like this: ``` dds <- DESeqDataSetFromMatrix(coun ...
deseq2 written 5 months ago by lihongfei930 • updated 5 months ago by Michael Love24k
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Comment: C: deseq2 analysis with multiple factors and interaction terms
... Hi Michael, I am doing similar analysis like him. But my question is I want to look at the differently expressed genes of treated/untreated samples between genotypeA/B. should I compute DEGs separately like: DEGs of genotypeA: treated/untreated, then DEGs of genotypeB: treated/untreated, at the end ...
written 5 months ago by lihongfei930

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