Moderator: russhh
russhh ♦ 5.4k
- Reputation:
- 5,440
- Status:
- Trusted
- Location:
- UK, U. Glasgow
- Twitter:
- @haematobot
- Last seen:
- 2 weeks ago
- Joined:
- 6 years, 2 months ago
- Email:
- r********@hotmail.com
Bioinformatics etc of leukaemia at University of Glasgow
Posts by russhh
<prev
• 794 results •
page 1 of 80 •
next >
1
vote
2
answers
182
views
2
answers
... This thread may get closed because you have shown relatively little effort.
But before it does, I think it's important that you identify part of bioinformatics, or part of the R/bioconductor ecosystem that is important/interesting to you. It will be extremely hard for you to write an interesting ta ...
written 4 weeks ago by
russhh ♦ 5.4k
0
votes
2
answers
182
views
2
answers
... How to contribute to Bioconductor ...
written 4 weeks ago by
russhh ♦ 5.4k
0
votes
0
answers
91
views
0
answers
... Is that surprising though? Your code works, but it is wrong. Let's suppose I'm a gene that is expressed at the same level in your four groups. Say my fitted value for treatment-group G, is `x + (noise_G)`. With your contrast as currently defined, the value of your contrast would be (x + noise_lesio ...
written 4 weeks ago by
russhh ♦ 5.4k
1
vote
0
answers
91
views
0
answers
... Rewrite your `design_factors`; eg, use `design_factors <- factor(make_names(design_labels))`. The column names of your design matrix are not the same as the levels used in your makeContrasts string. ...
written 4 weeks ago by
russhh ♦ 5.4k
1
vote
1
answer
222
views
1
answers
... Are the ensembl IDs that you are working with derived from the current ensembl release? ...
written 4 weeks ago by
russhh ♦ 5.4k
1
vote
1
answer
116
views
1
answers
Comment:
C: reactomePA error input file
... On a tibble or data.frame, the `[[` function extracts a column as a vector: `` `[[`(my_df, column_index)``. It takes the data.frame and a column index as argument; so when it's used as an operator it should look like `my_df[[column_index]]` (not `my_df[[, column_index]]`) ...
written 4 weeks ago by
russhh ♦ 5.4k
1
vote
1
answer
116
views
1
answers
Comment:
C: reactomePA error input file
... No, the code should be `genes <- d[[2]]; names(genes) <- d[[1]]` ...
written 4 weeks ago by
russhh ♦ 5.4k
0
votes
1
answer
116
views
1
answers
Comment:
C: reactomePA error input file
... There are several other ways of doing this mentioned in that SO thread, dplyr::pull for example ...
written 4 weeks ago by
russhh ♦ 5.4k
1
vote
1
answer
116
views
1
answers
Comment:
C: reactomePA error input file
... Plus, if you already have `tibble` loaded, you can use it's `deframe` function to do this in one step: https://stackoverflow.com/a/56479548/1845650 ; `genes <- tibble::deframe(d)` . That only works for two-column data-frames: the first column becomes the vector-names and the second column becomes ...
written 4 weeks ago by
russhh ♦ 5.4k
0
votes
1
answer
116
views
1
answers
Answer:
A: reactomePA error input file
... unlike when you subset a data-frame, when you subset a tibble using `tbl[, col]` syntax, you always receive a tibble.
For a data.frame, extracting a single column in this way would return a vector.
What you've done is extract geneList as a Nx1 tibble, and tried to set the names on that.
To extract ...
written 4 weeks ago by
russhh ♦ 5.4k
Latest awards to russhh
Commentator
7 weeks ago,
created a comment with at least 3 up-votes.
For C: fisher test with multiple samples
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question
11 weeks ago,
created a question with more than 1,000 views.
For setting up MArrayLM objects for use in RUnit tests
Teacher
11 weeks ago,
created an answer with at least 3 up-votes.
For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Appreciated
7 months ago,
created a post with more than 5 votes.
For C: Venn/Euler Diagram Of Four Or More Sets
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
7 months ago,
created a question with more than 1,000 views.
For Mouse decoy assembly
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question
11 months ago,
created a question with more than 1,000 views.
For setting up MArrayLM objects for use in RUnit tests
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
Commentator
12 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
Commentator
12 months ago,
created a comment with at least 3 up-votes.
For C: fisher test with multiple samples
Commentator
13 months ago,
created a comment with at least 3 up-votes.
For C: fisher test with multiple samples
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question
14 months ago,
created a question with more than 1,000 views.
For setting up MArrayLM objects for use in RUnit tests
Appreciated
14 months ago,
created a post with more than 5 votes.
For C: Venn/Euler Diagram Of Four Or More Sets
Commentator
16 months ago,
created a comment with at least 3 up-votes.
For C: fisher test with multiple samples
Good Answer
17 months ago,
created an answer that was upvoted at least 5 times.
For A: R survival analysis
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 717 users visited in the last hour