User: c.nicole

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c.nicole30
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Location:
Philadelphia
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1 year ago
Joined:
1 year ago
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c**********@uphs.upenn.edu

Posts by c.nicole

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Comment: C: Time course analysis in DESeq2: handling common baseline for two experimental co
... You're absolutely right - I passed the wrong DESeqResults object. After correction, the number of sig genes is the same pre and post lfcShrink(). Thank you! ...
written 12 months ago by c.nicole30
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Comment: C: Time course analysis in DESeq2: handling common baseline for two experimental co
... I'm using DESeq2 v 1.16.1 so I believe the default is betaPrior = FALSE so I'll need to use the lfcShrink(). When I do this, the number of significant genes is MUCH higher than results using the unshrunken LFC and I was confused but after reading this and this it seems like I should "use the p-value ...
written 12 months ago by c.nicole30
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Comment: C: Time course analysis in DESeq2: handling common baseline for two experimental co
... My solution for now is: 1. Remove the control 0 data 2. Use a ~group model --> injury_1, injury_3, injury_7, etc 3. Use design = ~group and run DESeq() [no test specification] 4. Use contrast to compare conditions on each day, ie: results(dds, contrast=c("group", "injury_1", "sham_1") You se ...
written 12 months ago by c.nicole30
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Comment: C: Time course analysis in DESeq2: handling common baseline for two experimental co
... Removed my first response because I realized it was answered in your response. I'll go ahead and drop the control_0 data from the analysis and try your first suggestion of constructing a contrast between sham and injury on each day. Thank you! ...
written 12 months ago by c.nicole30
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Time course analysis in DESeq2: handling common baseline for two experimental conditions
... Hello, I'm trying to perform a time course analysis of RNAseq data to identify genes that are differentially expressed as a function of experimental condition/how they change over time however, I have an unbalanced experimental design. I've read through the documentation, vignettes and various post ...
timecourse deseq2 differential gene expression multiple factor design rnaseq analysis written 12 months ago by c.nicole30 • updated 12 months ago by Gavin Kelly560

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