User: swbarnes2

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swbarnes2340
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Posts by swbarnes2

<prev • 97 results • page 2 of 10 • next >
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Answer: A: bwa mem to feature Counts
... I'm pretty sure bwa-mem is not splice aware, so it's not suitable for RNASeq. You really should use STAR. ...
written 7 weeks ago by swbarnes2340
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Answer: A: DEseq2 design for knockdown conditions and treatment
... You really need to also state how you called results, for anyone to know what results you are extracting. You seem to be asking for two different things. If you really want genes where (control-treated/control-vehicle)/ (target-control/target-vehicle) is far from 1, then the interaction term is th ...
written 8 weeks ago by swbarnes2340
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Comment: C: Responder Vs Non-Responders Paired Comparison DESeq2
... No one really wants to hold your hand through how to use the software. You will get better answers if you read through some DESeq tutorials, write some code using the examples you see, and ask about specific lines that you think might not be doing what you want them to. ...
written 9 weeks ago by swbarnes2340
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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 9 weeks 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 10 weeks 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 10 weeks 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 10 weeks 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 11 weeks 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 11 weeks 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 11 weeks ago by swbarnes2340

Latest awards to swbarnes2

Scholar 3 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 4 months ago, voted at least 25 times.
Scholar 11 months ago, created an answer that has been accepted. For C: Principal components in DESeq2
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Appropriate experimental design for differential expresion

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