User: sugus

gravatar for sugus
sugus20
Reputation:
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Status:
New User
Location:
China Pharmaceutical University
Last seen:
1 week, 1 day ago
Joined:
1 year, 11 months ago
Email:
6********@qq.com

Posts by sugus

<prev • 29 results • page 1 of 3 • next >
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Comment: C: How to remove batch effect in copy number segment mean
... Because it is a Pan Cancer analysis and it may have a batch effect. ...
written 4 weeks ago by sugus20
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How to remove batch effect in copy number segment mean
... Hi there, I am wondering how to remove batch effect on segmented_scna data downloading from TCGA PANCANA project. The demo of data format is as following: Sample Chromosome Start End Num_Probes Segment_Mean TCGA-KL-8323-11A-01D-2308-01 1 3218610 104558357 58272 0.0026 TCGA-KL-8323-11A- ...
cna segment combat batch effect written 4 weeks ago by sugus20
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Comment: C: ANNOVAR annotate frameshift
... Thank you for pointing this out but actually what's wrong is my input format. I have solved this problem and attached the solution below. Thanks again, Kevin. ...
written 7 weeks ago by sugus20
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Answer: A: ANNOVAR annotate frameshift
... I have solved this problem actually my input data format for ANNOVAR is wrong. For those two insertion, it should change the end postion and the "-" to the following: 14 69257040 69257040 - GG 14 69257144 69257144 - CC and if the mutation is a deletion, the end postion should correspond t ...
written 7 weeks ago by sugus20
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ANNOVAR annotate frameshift
... Hi there, I met a problem when annotate a nonframshift substitution but it was supposed to be frameshilt. Here is the example of data (test.avinput) and code. my data and the confusing annotations are the last two which I thought they were supposed to be frameshift. 14 69256505 69256505 G A ...
annovar mutation variant exonic written 7 weeks ago by sugus20
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extract gseaResult in clusterprofiler
... Hi there, My question is how to extract informtation of a specific pathway from gseaResult object derived from GSEA() in clusterProfiler R package. Basicly, I can just use gesaplot to plot what I am interested in gseaResult, but I want to output a detailed information of this specific pathway. How ...
clusterprofiler gsea written 11 weeks ago by sugus20 • updated 10 weeks ago by Guangchuang Yu2.0k
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Comment: C: GSEA results change in clusterProfiler
... Actually nothing happened when I set logical seed. The results still change. ...
written 11 weeks ago by sugus20
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Comment: C: GSEA results change in clusterProfiler
... OMG it should be logical, how stupid I am.... Thanks for pointing out that and let me try. ...
written 3 months ago by sugus20
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Comment: C: GSEA results change in clusterProfiler
... Thanks Yu, but how to get detailed information for each pathway. For example, GSEA output could be summary to a data frame with a lot of pathways, but gseaplot shall extract information from one of these pathway to plot figure, how to get this kind of information? Thanks advanced. ...
written 3 months ago by sugus20
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GSEA results change in clusterProfiler
... Hi there, Actually I have two questions, First, how to extract detail information from a GSEA object derived from GSEA() {clusterPorfiler R package}. Like the cmd: GSEA.RES <- GSEA(geneList = geneList,TERM2GENE=MSigDB,seed = 111,verbose=F) I have to use gseaplot and point the interested p ...
clusterprofiler gsea written 3 months ago by sugus20 • updated 3 months ago by Guangchuang Yu2.0k

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Scholar 7 weeks ago, created an answer that has been accepted. For A: ANNOVAR annotate frameshift

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