User: kumimesy

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kumimesy0
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Posts by kumimesy

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Comment: C: Network plot from expression data in R using igraph
... OK, thank you very much for your kind help! I wish you success and happiness. ...
written 10 days ago by kumimesy0
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Comment: C: Network plot from expression data in R using igraph
... Sure, I specified my original dataframe into the command. But it does not work. However, as you suggested, when I skipped that part and specified vertex sizes manually, it worked! Thank you so much. By the way, two thirds of my nodes don't have any edges. Could you let me know how to delete nodes wi ...
written 10 days ago by kumimesy0
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Comment: C: Network plot from expression data in R using igraph
... Yes, the original "simplify" command works well when I load igraph only. However, vSizes are still NA. Maybe it is caused by NA in my data, as you suggested earlier. Could you let me know the method to deal with NA problem? Thanks! ...
written 10 days ago by kumimesy0
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Comment: C: Network plot from expression data in R using igraph
... It works with your suggestion "g <- igraph::simplify(g, remove.multiple=TRUE, remove.loops=TRUE)". Thanks! Before you suggested the new graph.adjacency command, all values of both edgeweights and vSizes were NA. After I used your new graph.adjacency command, edgeweights are not NA. But all vSize ...
written 11 days ago by kumimesy0
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Comment: C: Network plot from expression data in R using igraph
... Thanks! I tried the command as you suggested, but in the next step of "g <- simplify(g, remove.multiple=TRUE, remove.loops=TRUE)", I still get the error message with "Error in simplify(g, remove.multiple = TRUE, remove.loops = TRUE) : unused arguments (remove.multiple = TRUE, remove.loops = TRUE ...
written 11 days ago by kumimesy0
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Comment: C: Network plot from expression data in R using igraph
... Hi Kevin, the command for graph.adjacency and the output of typing "g" at the console is as below. I found that there are 196 NAs in my data. My data is normalized microarray data of blood from 661 human subjects. When there are NAs, do I need to add specific argument? I also found that when I enter ...
written 11 days ago by kumimesy0
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Comment: C: Network plot from expression data in R using igraph
... Thank you Kevin, when I run graph.adjacency(), there was no error message. Although I viewed the list "g", it was difficult for me to know whether it was successful or not. Could you please let me know how to check the output of graph.adjacency()? ...
written 12 days ago by kumimesy0
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Comment: C: Network plot from expression data in R using igraph
... Hi, I tried "Step 2 Create the graph and tree objects" with my own microarray data. But values such as edgeweights and vSizes are all NA, and therefore I cannot get a plot with the error message of "need finite 'xlim' values. My own data is 182 obs. of 661 variables. Is there anything that I should ...
written 12 days ago by kumimesy0

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