User: giuseppe0525

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Posts by giuseppe0525

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Comment: C: TOMplot error: "color" is not a graphical parameter (WGCNA)
... Thank you very much! I didn't notice it. ...
written 6 months ago by giuseppe05250
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TOMplot error: "color" is not a graphical parameter (WGCNA)
... Hi, I met an error when using the TOMplot function of WGCNA. The plot was not labeled with any color and the following warning messages were returned: Warning messages: 1: In doTryCatch(return(expr), name, parentenv, handler) :   "colors" is not a graphical parameter 2: In doTryCatch(return(expr), ...
software error wgcna package written 6 months ago by giuseppe05250 • updated 6 months ago by Peter Langfelder1.8k
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Comment: C: gseaplot() function of clusterProfiler went wrong
... As 'Language "ca" is not one of the supported languages ['en']!' , I cannot list some objects mentioned above. ...
written 17 months ago by giuseppe05250
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gseaplot() function of clusterProfiler went wrong
... Hello, everyone! 1. I got the error 'Error in if (abs(max.ES) > abs(min.ES)) { :   missing value where TRUE/FALSE needed'  when running gseaplot() to visualize the GSEA result.   2. I run the code 'gseaplot(gsea, geneSetID = "mmu03013")'  where gsea is a gseaResult object. The class of gse ...
clusterprofiler gsea written 17 months ago by giuseppe05250
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Comment: C: GSEA using clusterProfiler
... Thank you very much for your help!   ...
written 17 months ago by giuseppe05250
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Comment: C: GSEA using clusterProfiler
... Thanks for your reply. In brief, I obtained the differentially expressed genes from microarray data based on Limma. The results are organized in a data frame with columns like gene ID, logFC, p value, adj. p value etc. In addition, I have the expression set from which I got the DEGs. The followi ...
written 17 months ago by giuseppe05250
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Answer: A: GSEA using clusterProfiler
... It seems that the problem resulted from the format of geneList, but I don't know how to create a data collection in the same format. I checked the example provided by the developer of the package and found that the geneList was a numeric vector whose element contained two numbers. One is the ID of ...
written 17 months ago by giuseppe05250
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GSEA using clusterProfiler
... Hello, everyone I 'm working on GSEA using clusterProfiler​ and came across two problems. 1. How should I prepare geneList​?  2. What does TERM2GENE mean​? I've worked out the differentially expressed genes from mouse microarray data. Then I tried the following script but failed to obtain the r ...
clusterprofiler gsea written 17 months ago by giuseppe05250
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Comment: C: question on GO analysis using clusterProfiler
... parts of the gene and universe as input are listed as followed:  > gene ## [1] "4312" "8318" "10874" "55143" "55388" "991" "6280" "2305" "9493" "1062" "3868" "4605" "9833" "9133" [15] "6279" "10403" "8685" "597" "7153" "23397" "6278" "79733" "259266" ...
written 17 months ago by giuseppe05250
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Comment: C: question on GO analysis using clusterProfiler
...   I have checked the coding of gene IDs and they were in Entrez ID. I used bitr() function to transform gene IDs and it worked well. " gene.df <- bitr(gene, fromType = "ENTREZID",                 toType = c("ENSEMBL", "SYMBOL"),                 OrgDb = org.Mm.eg.db) head(gene.df) " ##  &g ...
written 17 months ago by giuseppe05250

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