User: swbarnes2

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swbarnes2330
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Posts by swbarnes2

<prev • 95 results • page 1 of 10 • next >
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Comment: C: DESeq2 analysis with multiple factors
... I can't make heads or tails of your coldata the way its formatted, but I'm not surprised that your three term design doesn't work. Won't each mouse belong to one batch and/or one condition? ...
written 3 days ago by swbarnes2330
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Comment: C: Anyone else having trouble with biomaRt (Oct 10, 2019)
... So is it just the rat database that's not working right? ...
written 10 days ago by swbarnes2330
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Comment: C: Anyone else having trouble with biomaRt (Oct 10, 2019)
... I added the mirror because it was what another older post recommended trying. Before that, I had no mirror, but `version = 97` ...
written 10 days ago by swbarnes2330
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Anyone else having trouble with biomaRt (Oct 10, 2019)
... I'm using a command line that should work fine, that worked fine all yesterday, and today it intermittently works. > ensembl = useEnsembl(biomart='ensembl', dataset="rnorvegicus_gene_ensembl", mirror = 'uswest') > sequences <- getBM(attributes=c('ensembl_transcript_id', 'external_ ...
biomart ensembl written 11 days ago by swbarnes2330 • updated 10 days ago by Mike Smith4.0k
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Answer: A: Paired t-test with DESeq2
... > I really need to know how to perform the latter because the core > facility who analysed my samples did this and apparently don't want to > disclose the code used at this stage. This isn't going to end well. If you are responsible for this project, you do the analysis, so when people ha ...
written 11 days ago by swbarnes2330
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Answer: A: DESeq2: compare all tpts to baseline and pull results table accordingly
... > I've seen many posts in relation to my question but they all included replicates So yours does not? The number of questions that start with "I don't have replicates" and end with good useful answers are few and far between. You do not need clever algorithms to compare one sample to one sampl ...
written 13 days ago by swbarnes2330
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Comment: C: Batch effects between different sequencing runs
... I'll also note for the future that being sequenced at different times doesn't really matter. You can put things on the sequencing instrument whenever you want, that doesn't introduce technical artifacts. Prepping the RNA on different days, making the libraries on different days, **that** adds tech ...
written 17 days ago by swbarnes2330
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Answer: A: Batch effects between different sequencing runs
... If "SequenceRun" is batch, this is hopelessly confounded. It doesn't matter that multiple groups are found in each batch, what matter is that all the members of each group are found in only one batch. ...
written 17 days ago by swbarnes2330
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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 20 days ago by swbarnes2330
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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 4 weeks ago by swbarnes2330

Latest awards to swbarnes2

Scholar 12 weeks ago, created an answer that has been accepted. For C: Principal components in DESeq2
Scholar 3 months ago, created an answer that has been accepted. For C: Principal components in DESeq2
Supporter 3 months ago, voted at least 25 times.
Scholar 10 months ago, created an answer that has been accepted. For C: Principal components in DESeq2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Appropriate experimental design for differential expresion

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