User: c.nicole

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c.nicole30
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Location:
Philadelphia
Last seen:
1 month, 2 weeks ago
Joined:
1 month, 3 weeks ago
Email:
c**********@uphs.upenn.edu

Posts by c.nicole

<prev • 5 results • page 1 of 1 • next >
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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 7 weeks 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 7 weeks 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 7 weeks 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 7 weeks 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 7 weeks ago by c.nicole30 • updated 7 weeks ago by Gavin Kelly510

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