## User: courtney.stairs

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2 years, 3 months ago
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#### Posts by courtney.stairs

<prev • 15 results • page 1 of 2 • next >
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... OK, will do, thanks for your help. ...
written 5 months ago by courtney.stairs0
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... Thanks Michael! I had looked at the results section, but I struggled with thinking about the provided examples in terms of time as they seem to be more based on conditions + genotypes and not with comparing to time 0. But I'll keep trying! (Hopefully) just a couple more things. When you say: > ...
written 5 months ago by courtney.stairs0
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... Hi Michael, Sorry: "if one would like to say which genes are upregulated in the mutant at time 15 **compared to the wild type at time 15** you must do a pairwise Wald test" Would this be written as: results(ddsTC, name="strainmut.minute15", test="Wald") Would this produce the same result a ...
written 5 months ago by courtney.stairs0
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... Hi Michael, Thanks for your reply! I do have some followups: > The minutexvs_0 coefficients are the changes over time for the reference level of strain (WT). I see, so there is no consideration of the mutant here. How is the reference strain determined? Is it alphabetical? Or is this when yo ...
written 5 months ago by courtney.stairs0
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... Hi there, I'm struggling a little bit with understanding how to interpret the heatmap output from the fission test data here: http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time-course-experiments First, I would like to just confirm that I ...
written 5 months ago by courtney.stairs0 • updated 5 months ago by Michael Love24k
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... Thanks Michael! I have added those changes to my code :) ...
written 5 months ago by courtney.stairs0
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... Wonderful! Thank you Herve!! Thank you for your description of the methods, i really appreciate it. I will give this a go and come back if I have any questions :) ...
written 5 months ago by courtney.stairs0
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... Hi there, I'm following along on the rnaseqGene tutorial using the fission package, and I was wondering why the x axis on the time course experiment in section 9 is categorical (that is, time 1-6) rather than in minutes. http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGe ...
written 5 months ago by courtney.stairs0
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... Hi there, I'm trying to use GenomicFeatures to extract the sequences upstream and downstream of my transcripts. I have loaded my GTF file, however, I'm not sure how to proceed. I'm trying to extract 150 bp upstream and downstream of each gene as well as the CDS itself. If this isn't possible, ...
written 6 months ago by courtney.stairs0 • updated 5 months ago by Hervé Pagès ♦♦ 14k
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... Thank you Michael!  I will think about this more and come back if I have any questions.  /Courtney   ...
written 2.2 years ago by courtney.stairs0

#### Latest awards to courtney.stairs

Popular Question 2.2 years ago, created a question with more than 1,000 views. For DESEQ2 'results' filter by value for multiple conditions (contrast off?)

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