User: swbarnes2

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swbarnes2340
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Posts by swbarnes2

<prev • 104 results • page 3 of 11 • next >
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Comment: C: How to align to genome and transcriptome coordinates at the same time with STAR?
... Did you try just running the command line as they described it? Or looking up what all those options do? ...
written 3 months ago by swbarnes2340
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Answer: A: rlog in reference level
... rlog values aren't used in calculating log fold changes. Size normalized values are. ...
written 3 months ago by swbarnes2340
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Comment: C: is our edgeR code doing what we think it does?
... Why is making the DGEList and calculating size factors in its own function? dgList$samples$lib.size <- colSums(dgList$counts) doesn't seem to do anything. I don't think the code after is doing much either. ...
written 3 months ago by swbarnes2340
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Answer: A: is our edgeR code doing what we think it does?
... Doing T-tests on logged CPM data...I guess if you really have nothing but Excel, it will give you an idea..but this is not how you are supposed to do it. You can't publish based on results like this. You should follow what the EdgeR tutorials say, and let that software's algorithms do their stuff. ...
written 3 months ago by swbarnes2340
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Answer: A: Design for introducing batch effect in DESeq2
... Do what the DESeq software recommends. Give DESeq raw counts, not some kind of batch corrected, and include batch as a factor in the design. ...
written 3 months ago by swbarnes2340
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Answer: A: gene Isoforms quantification using RNA-seq data
... I think Salmon and Kallisto will quantify isoforms as well, but I don't think any of those are available through bioconductor ...
written 3 months ago by swbarnes2340
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Answer: A: How to perform RNA-seq with such MDS plot?
... Forget batch effect, it looks confounded with donor. So you have 3 donors for each cell-type/treatment combo, one of those donors is much different from the other two. You likely don't have the power to see the differences you want to see. Differences between donors swamps the differences between ...
written 3 months ago by swbarnes2340
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Comment: C: Comparison between two different group's pathway analysis results
... From your gprofiler link > g:GOSt performs functional enrichment analysis, also known as > over-representation analysis (ORA) or gene set enrichment analysis, on > input gene list. And it seems to have just one "Run query button" ...
written 3 months ago by swbarnes2340
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Comment: C: Two controls in RNAseq formula for DESeq2
... Okay, so you observed this: > The key point to remember about designs with interaction terms is > that, unlike for a design ~genotype + condition, where the condition > effect represents the overall effect controlling for differences due > to genotype, by adding genotype:condition, the ...
written 4 months ago by swbarnes2340
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Comment: C: Two controls in RNAseq formula for DESeq2
... Sorry, I misspoke in my answer. But your question is incomplete without saying exactly what comparison you are asking for in results, because the default is going to be to give you the genes which respond differently to treatment between sex, and it's not at all clear to me that that's what you rea ...
written 4 months ago by swbarnes2340

Latest awards to swbarnes2

Scholar 4 months ago, created an answer that has been accepted. For C: Principal components in DESeq2
Scholar 4 months ago, created an answer that has been accepted. For C: Principal components in DESeq2
Supporter 5 months ago, voted at least 25 times.
Scholar 12 months ago, created an answer that has been accepted. For C: Principal components in DESeq2
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Appropriate experimental design for differential expresion

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