User: courtney.stairs

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Posts by courtney.stairs

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Comment: C: DESEQ2 - help with interpreting time series heatmaps and resultsName
... OK, will do, thanks for your help. ...
written 5 weeks ago by courtney.stairs0
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Comment: C: DESEQ2 - help with interpreting time series heatmaps and resultsName
... 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 weeks ago by courtney.stairs0
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Comment: C: DESEQ2 - help with interpreting time series heatmaps and resultsName
... 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 weeks ago by courtney.stairs0
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Comment: C: DESEQ2 - help with interpreting time series heatmaps and resultsName
... 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 weeks ago by courtney.stairs0
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DESEQ2 - help with interpreting time series heatmaps and resultsName
... 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 ...
deseq2 written 6 weeks ago by courtney.stairs0 • updated 5 weeks ago by Michael Love23k
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Comment: C: DESEQ2: rnaseqGene fisison tutorial time course graph has non-numerical x-axis
... Thanks Michael! I have added those changes to my code :) ...
written 6 weeks ago by courtney.stairs0
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Comment: C: Using GenomicFeatures to extract the upstream and downstream region of a transcr
... 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 6 weeks ago by courtney.stairs0
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DESEQ2: rnaseqGene fisison tutorial time course graph has non-numerical x-axis
... 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 ...
deseq2 rnaseqgene written 6 weeks ago by courtney.stairs0
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Using GenomicFeatures to extract the upstream and downstream region of a transcript
... 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, ...
genomicfeatures written 9 weeks ago by courtney.stairs0 • updated 6 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: DESEQ2 'results' filter by value for multiple conditions (contrast off?)
... Thank you Michael!  I will think about this more and come back if I have any questions.  /Courtney   ...
written 22 months ago by courtney.stairs0

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