User: russhh
russhh • 4.1k
- Reputation:
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- UK, U. Glasgow
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- @haematobot
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Bioinformatics etc of leukaemia at University of Glasgow
Posts by russhh
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150
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... Your output isn't a data-frame, it has different vector lengths for each entry. Could you confirm why 13 is in the output for `B` given that it was absent from the input; and why 35 was filtered out of column C given that it is absent from column A. You might be better to generate a data.frame wit ...
written 12 days ago by
russhh • 4.1k
2
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1
answer
67
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1
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... Library size is dependent upon the genes included. In the simplest setting, for a given gene in a given sample the negative-binomial model effectively models the number of counts observed (for that gene) relative to the number of reads observed in total (for that sample). If you change the library s ...
written 12 days ago by
russhh • 4.1k
3
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0
answers
65
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0
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Comment:
C: Microaaray data analysis
... Disease association doesn't really imply disease involvement. And you have to be able to reproducibly show that your genes are discriminatory or you multi-gene signature is valid before you get to call them/it a biomarker. Depending on the application (early detection, prognosis, ...), very few biom ...
written 12 days ago by
russhh • 4.1k
0
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0
answers
91
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0
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... why can't you just use the MR values as a distance? It might not be subadditive ...
written 15 days ago by
russhh • 4.1k
1
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0
answers
377
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... could you post a bit more detail regarding your own research background, where the project will be based, whether the student will need to secure their own funding, whether they can work at-distance, please. ...
written 16 days ago by
russhh • 4.1k
0
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0
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129
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... are there differences in the library-sizes between your treatment-groups? ...
written 16 days ago by
russhh • 4.1k
2
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2
answers
105
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2
answers
... if you have
`rows <- c(100, 876, 438, ... 997 other entries ...)`
then `my_matrix[rows, ]` is how you 'submatrix-by-row-index'. In R you can index by either rownames or indices, or a boolean 'mask' vector (here it would be a vector of FALSEs with TRUE at the 100th, 438th, 876th and the other 997 ...
written 16 days ago by
russhh • 4.1k
1
vote
1
answer
213
views
1
answers
... my_cor <- apply(my_cpm, 1, function(x){cor(x,count["ENSG00000000005.5",], method = "spearman")})
I don't think plotting the correlation coefs would be particularly revealing; but you can do it if you want ...
written 18 days ago by
russhh • 4.1k
0
votes
1
answer
213
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1
answers
... Set the `method` argument. See here: https://www.rdocumentation.org/packages/stats/versions/3.5.1/topics/cor ...
written 18 days ago by
russhh • 4.1k
0
votes
1
answer
117
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1
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... Have you looked at it's docs yet? ...
written 20 days ago by
russhh • 4.1k
Latest awards to russhh
Teacher
8 days ago,
created an answer with at least 3 up-votes.
For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Appreciated
9 weeks ago,
created a post with more than 5 votes.
For C: Venn/Euler Diagram Of Four Or More Sets
Teacher
9 weeks ago,
created an answer with at least 3 up-votes.
For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher
10 weeks ago,
created an answer with at least 3 up-votes.
For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Appreciated
3 months ago,
created a post with more than 5 votes.
For C: Venn/Euler Diagram Of Four Or More Sets
Appreciated
6 months ago,
created a post with more than 5 votes.
For C: Venn/Euler Diagram Of Four Or More Sets
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Commentator
7 months ago,
created a comment with at least 3 up-votes.
For C: fisher test with multiple samples
Commentator
7 months ago,
created a comment with at least 3 up-votes.
For C: fisher test with multiple samples
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Has the RNA-Seq Atlas website closed?
Popular Question
10 months ago,
created a question with more than 1,000 views.
For VariantAnnotation parallel usage
Good Answer
11 months ago,
created an answer that was upvoted at least 5 times.
For A: R survival analysis
Appreciated
11 months ago,
created a post with more than 5 votes.
For C: Venn/Euler Diagram Of Four Or More Sets
Commentator
11 months ago,
created a comment with at least 3 up-votes.
For C: fisher test with multiple samples
Appreciated
12 months ago,
created a post with more than 5 votes.
For C: Venn/Euler Diagram Of Four Or More Sets
Good Answer
13 months ago,
created an answer that was upvoted at least 5 times.
For A: R survival analysis
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