User: ramiro.barrantes

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10
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New User
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United States
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1 year, 5 months ago
Joined:
2 years, 6 months ago
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r***************@uvm.edu

Posts by ramiro.barrantes

<prev • 6 results • page 1 of 1 • next >
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Deseq2 independent filtering not relevant for my data?
... Hello, When running DESeq2, I have some data and some genes with VERY low-pvalues (e.g. 3.12077x10^-8) were being filtered out with independent filtering, I looked more into it and found something that seems unusual.  I looked at the filtering cutoffs and they mostly low with one exception:  5.837 ...
deseq2 written 2.2 years ago by ramiro.barrantes10 • updated 10 days ago by Michael Love15k
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Comment: C: DESeq2 results are completely different for the same contrast when considering d
... Thanks so much.  This was the answer!!!  I have been doing the ph525.5x course by the way, it's been really helpful so thanks so much for that as well. ...
written 2.5 years ago by ramiro.barrantes10
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Comment: C: DESeq2 results are completely different for the same contrast when considering d
... oh and with respect to: "This is what you'd expect -- basically when you don't include "Gender" in your model, there is a source of variability that the model can not account for, and therefore can not make a significance call. When "Gender" is included, you acknowledge (and control for) difference ...
written 2.5 years ago by ramiro.barrantes10
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Comment: C: DESeq2 results are completely different for the same contrast when considering d
... Hi Steve, Thank you very much for your answer, it was very helpful.  I did as you suggested, let me paste again the data for this gene:                  expr Treatment Gender 1                   1      Cont      F 2                   1      Cont      F 3                   1      Cont      F 4      ...
written 2.5 years ago by ramiro.barrantes10
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DESeq2 results are completely different for the same contrast when considering different designs
... Hello, I am running DESeq2 on an experiment with Treatment (5 of them) and Gender (F and M) as part of the design. Everything runs ok but I am puzzled about some of the results.  I was comparing the results with DESeq and in the process ran it once with Treatment only and separately with Treatment ...
deseq2 written 2.5 years ago by ramiro.barrantes10 • updated 2.5 years ago by Steve Lianoglou12k
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On DESeq, Extracting specific comparisons from multifactor designs
... Hello, I have a multi-factor design and I have successfully used DESeq2 to extract my comparisons of interest.  I wanted to use DESeq1 in order to compare (long story) but I do not know how to extract specific comparisons.  THere is actually the following comment on the vignette: "Fixme: Can we ad ...
deseq deseq2 written 2.5 years ago by ramiro.barrantes10 • updated 2.5 years ago by Ryan C. Thompson6.1k

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