User: sugus
sugus • 20
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- China Pharmaceutical University
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- 1 week, 1 day ago
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- 1 year, 11 months ago
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Posts by sugus
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... Because it is a Pan Cancer analysis and it may have a batch effect. ...
written 4 weeks ago by
sugus • 20
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... 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- ...
written 4 weeks ago by
sugus • 20
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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
sugus • 20
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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
sugus • 20
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... 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
...
written 7 weeks ago by
sugus • 20
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... 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 ...
written 11 weeks ago by
sugus • 20
• updated
10 weeks ago by
Guangchuang Yu • 2.0k
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... Actually nothing happened when I set logical seed. The results still change. ...
written 11 weeks ago by
sugus • 20
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... OMG it should be logical, how stupid I am....
Thanks for pointing out that and let me try.
...
written 3 months ago by
sugus • 20
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... 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
sugus • 20
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... 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 ...
written 3 months ago by
sugus • 20
• updated
3 months ago by
Guangchuang Yu • 2.0k
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