User: kotcha.m

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kotcha.m0
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Posts by kotcha.m

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Comment: C: Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
... I see. Thank you so much! ...
written 4 months ago by kotcha.m0
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Comment: C: Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
... Hi Michael, I have another question. I want to compare the expression of M37 to M25, but both samples are first normalized to their WT counterparts. In other words, it'd be (M37 RPF/RNA)/(W37 RPF/RNA) / (M25 RPF/RNA)/(W25 RPF/RNA). Can I directly do this from design_1 like this?: results(all.DGE_ ...
written 4 months ago by kotcha.m0
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Comment: C: Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
... Alright. Thank you so much for your help! ...
written 4 months ago by kotcha.m0
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Comment: C: Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
... For design_1? It is there in the resultsNames. But in the text when I wrote out the list(), I made a mistake and dropped "type". Sorry about that! I'll edit it. ...
written 4 months ago by kotcha.m0
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Comment: C: Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
... Hi Michael, Thank you for your explanation. Let me see if I get this correctly.  design_1 = ~condition + condition:type > resultsNames(all.DGE_1) [1] "Intercept" "condition_M25_vs_W25" "condition_M37_vs_W25" "condition_W37_vs_W25" "conditionW25.typeRPF" [6] "conditionM25.typeRPF" "c ...
written 4 months ago by kotcha.m0
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Comment: C: Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
... Update: I just found another post that addressed almost the same questions: https://support.bioconductor.org/p/110259/ It seems that I got the design backwards? So, I changed it to design = ~condition + condition:type. (Side question, is ~condition + condition:type the same as ~condition + type + ...
written 4 months ago by kotcha.m0
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Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
... Dear Bioconductor support community, I have ribosome profiling/RNA-seq data that I want to analyze using DESeq2, but I am having some trouble with the design and how to compare selected samples. I'd really appreciate your help! I have 4 different conditions: 2 strains grown at 2 temperatures, each ...
sequencing deseq2 multiple factor design ribosome profiling riboseq written 4 months ago by kotcha.m0 • updated 4 months ago by Michael Love20k
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Comment: C: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
... Hi Michael, Thank you for your reply. I actually found another post that you have answered (https://support.bioconductor.org/p/110259/) that I think helped answer my questions. I will repost this question anyway though, along with the update of what I changed after reading the said post, because I ...
written 4 months ago by kotcha.m0
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Comment: C: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
... Hi Michael, I have a slight variation of the ribosome profiling/RNA-seq data above so I will just ask my questions here. I'd really appreciate your help! I have 4 different conditions: 2 strains grown at 2 temperatures, each condition has ribo-seq and RNA-seq data, and two replicates for each. Fro ...
written 4 months ago by kotcha.m0

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