User: swbarnes2

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swbarnes250
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Posts by swbarnes2

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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... The samples in your counts excerpt that you labeled "control" have the size factors associated with treat1 from colData.  Let me guess.  You made the group column by copying and modifying a command line from a tutorial, without understanding what you were doing? ...
written 13 hours ago by swbarnes250
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... What do you get from colData(dds)?  ​I still think you have mixed up the labeling of your samples, as those Log2Fold changes look more like treat1/treat2. ...
written 1 day ago by swbarnes250
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Answer: A: deseq2 analysis multiple factor and 4 different time points
... You make dds from raw counts, not normalized.  I'm not even sure what happens if you try to make a dds object with non-integer counts as input.   That method of making a concatenated "group" column is useful for comparing subsets of samples to each other, while using the dispersion of the whole da ...
written 5 days ago by swbarnes250
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Multiple tissue types in one DESeq2 object
... I have a project with 20 samples of one tissue, and 20 of another.  (also, there are two different genotypes, and 2 different treatments) I was wondering if I should be keeping them together as a single DEseq object if the investigators are not really interested in comparing between tissues.  I was ...
deseq2 written 18 days ago by swbarnes250 • updated 18 days ago by Michael Love19k
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Answer: A: Why does biomart work on humans and not mouse genes for HGNC symbol conversion?
... I'm going to guess your problem is this: https://www.genenames.org/ "HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication."   When I use the little search bar in the c ...
written 5 weeks ago by swbarnes250
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Comment: C: Strange results from Deseq2
... Yeah, I realized that after I wrote it.  Thanks again. ...
written 9 weeks ago by swbarnes250
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Comment: C: Strange results from Deseq2
... Thanks, I tried some things, and added a follow-up in my question ...
written 9 weeks ago by swbarnes250
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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 9 weeks ago by swbarnes250
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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 weeks ago by swbarnes250
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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 3 months ago by swbarnes250

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