User: courtney.stairs

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Posts by courtney.stairs

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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 12 days ago by courtney.stairs0
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Comment: C: DESEQ2 'results' filter by value for multiple conditions (contrast off?)
... Hi Michael,  Thanks for your reply.  I'd like to use this as a method to see genes that are differentially expressed in each condition versus the control condition.   I expect some genes to respond similarly to each treatment while others to either be inversely regulated or unchanged.   My ultimate ...
written 12 days ago by courtney.stairs0
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Comment: C: DESEQ2 'results' filter by value for multiple conditions (contrast off?)
... To extend on this observation, I redid the analysis with the LRT and found that now each comparison has the same number of values where each gene has the same padj but different fold-change (depending on the condition). So would you recommend when doing a 'two (or more) treatments vs control' experi ...
written 13 days ago by courtney.stairs0
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DESEQ2 'results' filter by value for multiple conditions (contrast off?)
... EDIT: I think this post might answer my question? https://www.biostars.org/p/115685/ Hi there, I was hoping for some clarification regarding the 'results' function of DESEQ2.  I see from the manual it says that if 'contrast' is not specified, it will return 'results'  from the last comparison.  I ...
deseq2 contrast padj results written 14 days ago by courtney.stairs0 • updated 13 days ago by Michael Love12k
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Comment: C: FeatureCounts output to SAM like htseq-counts?
... Great! Thank you!  I'll keep an eye out!   ...
written 5 weeks ago by courtney.stairs0
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FeatureCounts output to SAM like htseq-counts?
... Hi there, I have been using featureCounts for quite some time now and I really like it.  However, I have come across a workflow for deconvoluting multimapping of RNAseq reads to multiple genes  (RNAfreak) that requires the output of htseq-counts since it gives a read summaries (i.e., the fate of ea ...
featurecounts sam htseqcounts written 6 weeks ago by courtney.stairs0

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