User: swbarnes2

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swbarnes230
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Posts by swbarnes2

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Strange results from Deseq2
... Yeah, I realized that after I wrote it.  Thanks again. ...
written 2 days ago by swbarnes230
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Comment: C: Strange results from Deseq2
... Thanks, I tried some things, and added a follow-up in my question ...
written 2 days ago by swbarnes230
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Strange results from Deseq2
... I'm getting strange results from DESeq2 results.  I'm comparing 3 samples to another group of 3 samples, which I know is less than ideal   counts<-read.csv("raw_180803.csv", header = TRUE, row.names = 1, check.names = FALSE) anno <- read.csv("anno_180803.csv", header = TRUE, row.names = 1) ...
deseq2 written 3 days ago by swbarnes230
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Comment: C: Individuals nested within blocks in DESeq2
... I don't understand the difference between ind and ind.n.  I suspect you don't need ind.n ...
written 10 days ago by swbarnes230
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Answer: A: 3x2 comparisons in DEseq - time (3 time points) and two treatments
... I think you might as well start by making a PCA plot of your samples...if you find that batch isn't having an effect, you might drop it as a design factor. ...
written 6 weeks ago by swbarnes230
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Answer: A: Understanding Contrasts when analyzing DESeq2 results
...  I don't think you should expect those two methods to return the same answer...though they both return that the fold change, if any, is very small, and the p-value is so bad, you would conclude in both cases that there is no significant difference.   At the very least, the first way, all samples a ...
written 6 weeks ago by swbarnes230
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Answer: A: A DESeq2 problem in dealing with case-control study
... Well, just kind of eyeballing your PCA plot, it looks like the most significant thing going on in your data isn't differences caused by treatment.  It's whatever is making those four or five samples separate from the rest.  Batch effect? So you should probably believe what DESeq2 is telling you. ...
written 10 weeks ago by swbarnes230
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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 3 months ago by swbarnes230
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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 4 months ago by swbarnes230
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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 4 months ago by swbarnes230

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