User: j.siefert

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j.siefert0
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Posts by j.siefert

<prev • 7 results • page 1 of 1 • next >
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Comment: C: DEseq2 design for knockdown conditions and treatment
... Ah yes, of course. Ok, thanks ...
written 4 weeks ago by j.siefert0
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Comment: C: DEseq2 design for knockdown conditions and treatment
... Sorry, one more quick question. If I wanted to look at { siC-T/siC-V : siT-T/siC-V } , and ignore the differences in the siT-V sample, what would be the design for that? ...
written 4 weeks ago by j.siefert0
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Comment: C: DEseq2 design for knockdown conditions and treatment
... Thanks for your comment. What I am looking for is the ratio between control-treated/control-vehicle and target-control/target-vehicle. I realize this isn't exactly "normalizing", but that's what I meant. After running: > dds <- DESeq(dds) I generated reults with: > res <- results(dds) ...
written 4 weeks ago by j.siefert0
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Comment: C: DEseq2 design for knockdown conditions and treatment
... That's what I was afraid of. Ok, thanks Michael ...
written 4 weeks ago by j.siefert0
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Comment: C: DEseq2 design for knockdown conditions and treatment
... I think I'm trying to do this: { siC-T/siC-V : siT-T/siT-V } ...
written 4 weeks ago by j.siefert0
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Comment: C: DEseq2 design for knockdown conditions and treatment
... Thanks for the quick reply and the comment. I didn't realize that the order of the factors specified the reference. What I would like to find is genes that are differentially expressed in the siTarget treated vs. the siControl treated. I know that there will be a lot of differentially expressed gen ...
written 4 weeks ago by j.siefert0
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DEseq2 design for knockdown conditions and treatment
... I have a question about the proper design for DEseq2, when there is an siControl as well as siRNA for a target gene, then there is a treated and a vehicle for both conditions. I setup the factors and design like so: > dds$condition <- factor(dds$condition, levels =c("siControl","siTarget ...
deseq2 written 4 weeks ago by j.siefert0 • updated 4 weeks ago by swbarnes2330

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