User: urwa

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urwa0
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Posts by urwa

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Comment: C: R: How to convert graphNEL object into Adjacency Matrix
... Thanks a lot! This was helpful! ...
written 19 months ago by urwa0
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Comment: C: R: How to convert graphNEL object into Adjacency Matrix
... `Error in as.character.default(from) : no method for coercing this S4 class to a vector In addition: Warning message: In coerce(mergedPathways_d, to = "matrix") : direct use of coerce() is deprecated: use as(from, class(to)) instead` ...
written 19 months ago by urwa0
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R: How to convert graphNEL object into Adjacency Matrix
... This is my graphNEL object `>mergedPathways_d` `A graphNEL graph with undirected edges` `Number of Nodes = 41` `Number of Edges = 102` I have tried `coerce`. It did not work out. It asks to pre-define the matrix and To and From didnot work correctly, I had NA as entries in my adj matrix I ...
R written 19 months ago by urwa0 • updated 7 months ago by Biostar ♦♦ 20
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R: objNameToList() on some particular list of objects in parent frame
... This is my graphNEL object `>mergedPathways_d` `A graphNEL graph with undirected edges` `Number of Nodes = 41` `Number of Edges = 102` I have tried `coerce`. It did not work out. It asks to pre-define the matrix and To and From didnot work correctly, I had NA as entries in my adj matrix I ...
R written 19 months ago by urwa0
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Comment: C: Merging Kegg Pathways
... Thanks a bunch. That was all I was looking for. I had one trouble though. My global environment has a lot of other values and datasets. So this command `pathways<-objNameToList(objects(), parent.frame())` those other files. I have clear global environment before running the above code snippet. ...
written 19 months ago by urwa0
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How to filter GSE series which have normalized log ratios for experimental cases and normal controls?
... A total of 128 GSE series are present in the GEO database for mycobacterium tuberculosis. I want to filter out those GSE series which have normalized log ratios for for experimental cases and normal controls. Is there a filter/option for that or do I need to download all 128 GSE and then look at the ...
geo gse log-ratio written 21 months ago by urwa0
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GEO series (GSE) - Filtering series with both disease and control samples
... There are 207 GEO series for mycobacterium tuberculosis. I want to filter those series which have both disease and control samples in it. Is there are smart way to do it or I have to do it manually by reading through every single one of them. ...
geo filters gse written 21 months ago by urwa0

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