User: nature.hunger

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Posts by nature.hunger

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Answer: A: only 0's may be mixed with negative subscripts
... These days I got an answer from your Pathview web server. Because it has no hsa04215 pathway in your web server. But it has hsa04215 pathway in KEGG website (http://www.kegg.jp/pathway/hsa04215). ...
written 8 months ago by nature.hunger0
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Comment: C: Got an confusing about BgRatio in enrichKEGG result of clusterprofiler
... Thanks! It works fine now!  ...
written 9 months ago by nature.hunger0
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Comment: C: Got an confusing about BgRatio in enrichKEGG result of clusterprofiler
... Thank you very much! It is the reason that I am not using the newest version of clusterProfilier. It might be the reason of my Bioconducter(V3.3) is not the newest version. So when I following the installation instructions as: source("https://bioconductor.org/biocLite.R") biocLite("clusterProfiler ...
written 9 months ago by nature.hunger0
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Comment: C: Got an confusing about BgRatio in enrichKEGG result of clusterprofiler
... Thanks. I have a another question. why setReadable function can't support in enrichKEGG function output with entrenz gene ID but can be used in uniprot ID. I had google that the  previously version had the readable parameter, but it is useless now. ...
written 9 months ago by nature.hunger0
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Comment: C: Got an confusing about BgRatio in enrichKEGG result of clusterprofiler
... Thanks a lot ! I am trying to imply it into differentially expression genes list from my projects. And I had try these two methods. The number of genes in the same enriched KEGG pathway are different and consequently results to the KEGG pathway rank differently. So that I can only put my gene list i ...
written 9 months ago by nature.hunger0
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Got an confusing about BgRatio in enrichKEGG result of clusterprofiler
... I am trying to runing the example of clusterprofiler from  "http://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html#abstract" and "https://guangchuangyu.github.io/2016/05/convert-biological-id-with-kegg-api-using-clusterprofiler/". I got an question in ...
clusterprofiler written 9 months ago by nature.hunger0 • updated 9 months ago by Guangchuang Yu700
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only 0's may be mixed with negative subscripts
... I got an Error about only 0's may be mixed with negative subscripts. I read a txt file as data.frame , it has more than 100 rows with 2 columns. And 4 genes are enriched in hsa04215 pathway. And I extract it from data.frame and transform to a vector, look like > xx       836       596      5599 ...
pathview written 9 months ago by nature.hunger0

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