Moderator: russhh
russhh ♦ 5.5k
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Bioinformatics etc of leukaemia at University of Glasgow
Posts by russhh
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... 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
russhh ♦ 5.5k
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... How to contribute to Bioconductor ...
written 4 months ago by
russhh ♦ 5.5k
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... 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
russhh ♦ 5.5k
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... 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
russhh ♦ 5.5k
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... Are the ensembl IDs that you are working with derived from the current ensembl release? ...
written 4 months ago by
russhh ♦ 5.5k
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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
russhh ♦ 5.5k
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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
russhh ♦ 5.5k
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279
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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
russhh ♦ 5.5k
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279
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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
russhh ♦ 5.5k
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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
russhh ♦ 5.5k
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