User: russhh
russhh • 3.2k
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- UK, U. Glasgow
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- @haematobot
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- Joined:
- 3 years, 11 months ago
- Email:
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Bioinformatics etc of leukaemia at University of Glasgow
Posts by russhh
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Comment:
C: metanalysis in R
... There's many questions related to this. For example, see [this][1] from yesterday
[1]: https://www.biostars.org/p/310089/ ...
written 1 day ago by
russhh • 3.2k
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... The contrasts are the same from a hypothesis testing perspective. I'd use the contrast 1 however (the difference between the averages) as the contrast coefficient that it returns will look like the difference on a log2 boxplot ...
written 11 days ago by
russhh • 3.2k
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95
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Comment:
C: Null hypothesis in DESeq2
... You are correct. Stop worrying and just do your experiment ...
written 12 days ago by
russhh • 3.2k
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Comment:
C: Null hypothesis in DESeq2
... What are you talking about? Significance is a technical term; a "significant gene" in the context of a hypothesis test for a given coefficient (or contrast) is one for which the probability of getting a more extreme observation under the conditions of the null hypothesis is less than your threshold. ...
written 13 days ago by
russhh • 3.2k
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Comment:
C: Null hypothesis in DESeq2
... Yes it does use null hypothesis-base significance testing. `X is not signficant` is not a statistical hypothesis; depending on your experimental setup / design etc the null used by DESeq2 would typically be that "Coefficient Y is zero for gene X". ...
written 13 days ago by
russhh • 3.2k
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... We can't really do anything with the information provided. Have you tried compiling the manual outside of R CMD build? ...
written 13 days ago by
russhh • 3.2k
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135
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... post it in your original question; and, rather than posting it in a non-copyable way, could you read [this][1] and post the output of using `dput`.
[1]: https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example ...
written 16 days ago by
russhh • 3.2k
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134
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... Will biostars be first author? ...
written 20 days ago by
russhh • 3.2k
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... Thanks for sharing your process. I think publication level queries are best kept off a Q&A site, seems a bit presumptuous to me. ...
written 20 days ago by
russhh • 3.2k
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... Then make-up some data that conforms to the data structure that you are working with <\!!!>
See the help for tidyr::gather and look what happens after each step of data-manipulation that I gave you. Those are the columns that are gathered into the Accuracy column (of the output data) from t ...
written 22 days ago by
russhh • 3.2k
Latest awards to russhh
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10 days ago,
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For C: fisher test with multiple samples
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For C: fisher test with multiple samples
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27 days ago,
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For A: Unexpected outcome: Gene Enrichment using Fisher's Test
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For Has the RNA-Seq Atlas website closed?
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For VariantAnnotation parallel usage
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4 months ago,
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For A: R survival analysis
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For C: Venn/Euler Diagram Of Four Or More Sets
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For C: fisher test with multiple samples
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For A: R survival analysis
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For A: Unexpected outcome: Gene Enrichment using Fisher's Test
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8 months ago,
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For A: Unexpected outcome: Gene Enrichment using Fisher's Test
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9 months ago,
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For C: Venn/Euler Diagram Of Four Or More Sets
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9 months ago,
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For A: Unexpected outcome: Gene Enrichment using Fisher's Test
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10 months ago,
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For C: fisher test with multiple samples
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For C: fisher test with multiple samples
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For A: scripting problem to use ProtComp output to identify secretome proteins
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