Moderator: russhh

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russhh5.5k
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Bioinformatics etc of leukaemia at University of Glasgow
 

Posts by russhh

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Answer: A: Any good idea for bioinfo final presentation?
... 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 months ago by russhh5.5k
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Comment: C: Any good idea for bioinfo final presentation?
... How to contribute to Bioconductor ...
written 4 months ago by russhh5.5k
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Comment: C: Calculating Contrast Matrix in Limma for Differential Expression
... 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 months ago by russhh5.5k
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Comment: C: Calculating Contrast Matrix in Limma for Differential Expression
... 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 months ago by russhh5.5k
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Comment: C: Ensembl ID to ENTREZ best converter
... Are the ensembl IDs that you are working with derived from the current ensembl release? ...
written 4 months ago by russhh5.5k
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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 months ago by russhh5.5k
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Comment: C: reactomePA error input file
... No, the code should be `genes <- d[[2]]; names(genes) <- d[[1]]` ...
written 4 months ago by russhh5.5k
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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 months ago by russhh5.5k
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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 months ago by russhh5.5k
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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 months ago by russhh5.5k

Latest awards to russhh

Commentator 5 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 5 months ago, created an answer that has been accepted. For C: muTect analysis, error
Popular Question 6 months ago, created a question with more than 1,000 views. For setting up MArrayLM objects for use in RUnit tests
Scholar 6 months ago, created an answer that has been accepted. For C: muTect analysis, error
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 7 months ago, created an answer that has been accepted. For C: muTect analysis, error
Appreciated 10 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Teacher 11 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 Mouse decoy assembly
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question 15 months ago, created a question with more than 1,000 views. For setting up MArrayLM objects for use in RUnit tests
Appreciated 15 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Appreciated 16 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
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 17 months ago, created an answer that has been accepted. For C: muTect analysis, error
Popular Question 18 months ago, created a question with more than 1,000 views. For setting up MArrayLM objects for use in RUnit tests
Appreciated 18 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: R survival analysis

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