User: sugus

gravatar for sugus
sugus40
Reputation:
40
Status:
New User
Location:
China Pharmaceutical University
Last seen:
1 month ago
Joined:
2 years, 10 months ago
Email:
6********@qq.com

Posts by sugus

<prev • 43 results • page 1 of 5 • next >
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Interpretation the percentage of top 10 mutated gene in plotmafSummary result
... Hi, I am learning maftools, a R package, to analyze some mutation data but I am really confused about the percentage of top 10 mutated gene in plotmafSummary result when reading your delicate vignette. I made a screenshot and show it as the follows: ![enter image description here][1] You could ob ...
R maftools mutation written 5 weeks ago by sugus40 • updated 5 weeks ago by dsull450
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Comment: C: GSEA results change in clusterProfiler
... Yeah, it is true that the result would change no matter what seed you set. But try to set the nPerm = 10000 instead of 1000 by default, and that would quite stable just like you set a seed! ...
written 7 weeks ago by sugus40
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Heatmap for GISTIC2.0
... Hi there, In the output of GISTIC2.0 algorithm for copy number analysis, there is a generated heatmap Segmented Copy Number (raw_copy_number.pdf and raw_copy_number.png). The png file is shown as the following: ![heatmap][1] This file is a heat map image of the segmented copy number profiles in ...
R cnv gistic2.0 heatmap written 10 weeks ago by sugus40 • updated 12 days ago by Biostar ♦♦ 20
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DMRcate results: How to interpret the overlapping.promoters
... Hi there, I am using CHAMP to perform differential methylation analysis, including DMP and DMR. Regarding DMR, I used DMRcate algorithm and I am a little bit confused about the result. In the derived table of DMRcate embedded in CHAMP, I got a column of overlapping.promoters. For example: ...
dna methylation dmrcate R champ written 11 weeks ago by sugus40
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Comment: C: How single sample GSEA works
... No, this parameter was just like it was. OMG it is really confusing... Maybe I should just calculate the average value for each signature and at least that would be more interpretable. ...
written 3 months ago by sugus40
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Mouse RNA-seq research
... Hi there, I have some mouse rna-seq data and would like to do some functional enrichment analysis, but I do not have such robust signatures designed just for mouse, such as MSigDB. Thus, I wonder is it logical to convert mouse gene to human gene, and perform the typical downstream analysis just li ...
mouse rna-seq human written 3 months ago by sugus40
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Comment: C: How single sample GSEA works
... Sorry the code is another test, the 'actual' score was calculated by ssgsea method. The heatmap showed the expression of all genes included in the first pathway, which show in the scoremap. I used specific gene list corresponding to a pathway to make a signature. In the meta.sig, there are 23 pathw ...
written 3 months ago by sugus40
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Comment: C: How single sample GSEA works
... Thanks, the meta.sig is a list contains 23 metabolism related pathways. Each element in the list is a vector of genes corresponding to the specific pathway. I am not asking the order because the order is fixed either in the heatmap or scoremap. I just wonder why the enrichment score would be totally ...
written 3 months ago by sugus40
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Comment: C: How to determine subtype-specific mutations?
... Maybe, thanks for reminding. ...
written 3 months ago by sugus40
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Comment: C: Using Varscan without a matched normal
... Yeah, i am working on this. Thanks for this sweet encouragement :) ...
written 3 months ago by sugus40

Latest awards to sugus

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Reorder dendrogram for a better heat map
Popular Question 3 months ago, created a question with more than 1,000 views. For No result in enrichGO
Popular Question 3 months ago, created a question with more than 1,000 views. For How to construct Bayesian regulatory network in R with gene expression profile
Popular Question 9 months ago, created a question with more than 1,000 views. For customized clusterAlg of NMF in consensusClusterPlus
Popular Question 9 months ago, created a question with more than 1,000 views. For How to get a matrix gene weights in NMF
Popular Question 9 months ago, created a question with more than 1,000 views. For No result in enrichGO
Scholar 13 months ago, created an answer that has been accepted. For A: ANNOVAR annotate frameshift

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