User: russhh

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russhh3.8k
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@haematobot
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Bioinformatics etc of leukaemia at University of Glasgow
 

Posts by russhh

<prev • 573 results • page 1 of 58 • next >
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Answer: C: GetBM gives controversial results
... set `chromosome_name` to `X` not `chrX` in your `getBM` ...
written 16 days ago by russhh3.8k
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243
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Comment: C: To make difference or Ratio, it's a problem
... Did you mean 'not ideal'? ...
written 16 days ago by russhh3.8k
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Comment: C: Geom_Bar: fill bars with a color gradient
... Good stuff - I was guessing ...
written 18 days ago by russhh3.8k
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Answer: A: Geom_Bar: fill bars with a color gradient
... Your code: ggplot( de_results_midline_highest_lowest [1:20,], aes(x = reorder (external_gene_name, norm_count_1), y = norm_count_1, fill= external_gene_name)) + geom_bar(position="dodge", stat="identity") + xlab("Gene") + ylab("Normalized Counts") + coord_flip()+ ...
written 18 days ago by russhh3.8k
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Comment: C: Adding data to R S4 object
... But then, you are doing exactly the same thing you've just been doing. The error is inside the source code for the `construct` function. You can get around it if you pass in a `samplevector` in addition to your `exprmatrix`. Try downloading the github repo for `sincera`, modify the line of code i to ...
written 5 weeks ago by russhh3.8k
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Comment: C: Adding data to R S4 object
... Looking at the source code for sincera it looks like you've found a bug (see line 99 of https://github.com/xu-lab/SINCERA/blob/master/R/sincera.R ). Post as issue via github and make a pull request: you just need to change `rexpr` to `rexprs`. Sincera is throwing the error because it can't find `rex ...
written 5 weeks ago by russhh3.8k
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Comment: C: Adding data to R S4 object
... in the code you've posted, you aren't replacing the values that are currently stored in `sc`; you are constructing a brand-new object and storing that in `sc`. It may be possible to hack it so that you can update the `rexpr` entry of the pre-existing `sc` using `sc@rexpr <- ipf.exprmatrix`. (I' ...
written 5 weeks ago by russhh3.8k
0
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Comment: C: How to know which samples are treated and untreated?
... but does that mean the patient was treated during follow-up, or does it mean the patient was treated prior to resection? ...
written 5 weeks ago by russhh3.8k
0
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Comment: C: How to know which samples are treated and untreated?
... To be honest, it doesn't look like the samples (strictly the patients they were derived from) were treated prior to resection, but I can't find any explicit statement. It is very unlikely the patients weren't treated after the surgery had been performed. ...
written 5 weeks ago by russhh3.8k
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Comment: C: Differentially expressed genes between sensitive and non sensitive with a simple
... your FDR was calculated based on random sampling; the reason you have zeros is because in none of the randomly-sampled runs was the sampled statistic greater than the observed value. You'd need 10000s of samples to get values greater than zero for your most-significant hits Do you know why your t-s ...
written 6 weeks ago by russhh3.8k

Latest awards to russhh

Appreciated 12 days ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Appreciated 6 weeks ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Appreciated 4 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 4 months ago, created an answer that has been accepted. For C: muTect analysis, error
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 6 months ago, created an answer that has been accepted. For C: muTect analysis, error
Popular Question 7 months ago, created a question with more than 1,000 views. For Has the RNA-Seq Atlas website closed?
Popular Question 9 months ago, created a question with more than 1,000 views. For VariantAnnotation parallel usage
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: R survival analysis
Appreciated 9 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Scholar 10 months ago, created an answer that has been accepted. For C: muTect analysis, error
Appreciated 11 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: R survival analysis
Scholar 12 months ago, created an answer that has been accepted. For C: muTect analysis, error
Scholar 12 months ago, created an answer that has been accepted. For C: muTect analysis, error
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 14 months ago, created an answer that has been accepted. For C: muTect analysis, error
Appreciated 14 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets

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