User: swbarnes2

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swbarnes210
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Posts by swbarnes2

<prev • 7 results • page 1 of 1 • next >
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Answer: A: DESeq2 design formula - how to account for donor and /or sample?
... Do not add "sample" to the design.  You can't add anything to the design if it's different in every single sample. ...
written 7 days ago by swbarnes210
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Answer: A: colData and design problem
... That treatment column is not helping.  Get rid of it.  If your control really is different form the uninjected, having only one isn't going to be very useful. ...
written 6 weeks ago by swbarnes210
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Comment: C: DESeq2 count normalization
... Would downsampling the sample with many times as many reads as the others be appropriate? ...
written 8 weeks ago by swbarnes210
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Comment: C: Adjusting for lane and index with DESeq2
... Are you sure that you need technical replicates, and to account for lanes and indices?  I don't think that most people do that. ...
written 9 weeks ago by swbarnes210
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Comment: C: How to handle strong batch effects
... But order doesn't actually matter in the design, right?  It only matters if you don't specify in the results what element you want to contrast? ...
written 10 weeks ago by swbarnes210
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Comment: C: DESeq2 Control for differences between patients
... Unadjusted p-values are not the right thing to be looking at.  Stick with adjusted p-values.  As always, XKCD explains why:  https://xkcd.com/882/ ...
written 10 weeks ago by swbarnes210
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Answer: A: DESeq2 Control for differences between patients
... You have 10 control samples and 10 treatment samples.  If you wanted to control for sex, or age (maybe by splitting the samples into a few age groupings) you could tell it that information, and make use of that, but it's already going to treat your samples as if they were biological replicates. ...
written 10 weeks ago by swbarnes210

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