User: Samuel Lee

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Samuel Lee0
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Posts by Samuel Lee

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Comment: C: STRING_id mismatch with STRINGdb
... I realised that the line ``` sum(example1_mapped$STRING_id %in% igraph::V(sgrph)) ``` should be ``` sum(example1_mapped$STRING_id %in% get.vertex.attribute(sgrph, "name")) # [1] 17528 ``` which does show that the vertex names are in fact comparable... sadly it doesn't get me any closer to worki ...
written 6 weeks ago by Samuel Lee0
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STRING_id mismatch with STRINGdb
... Hi, I'm trying to use STRINGdb for parsing the STRING PPI network in R. However, I've run into an issue where the `get_neighbors()` method fails with the following error `Error in as.igraph.vs(graph, v) : Invalid vertex names`. It seems non of the mapped `STRING_id`'s are included in the graph despi ...
stringdb igraph written 6 weeks ago by Samuel Lee0
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Comment: C: how to infer missing PAM50 molecular subtypes in TCGA-BRCA dataset downloaded wi
... Hi Patricia, Did you ever find an answer to where the subtype_PAM50.mRNA assignments come from? I've been wondering this for a while now so any insights you've gained would be appreciated! Thanks, Sam ...
written 6 months ago by Samuel Lee0

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