User: liu4gre

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liu4gre200
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1 year, 9 months ago
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Posts by liu4gre

<prev • 61 results • page 1 of 7 • next >
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Comment: C: cox proportional hazard model
... Thanks. Nice tutorial. ...
written 22 months ago by liu4gre200
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Comment: C: cox proportional hazard model
... Great, thanks. Sorry for one more question. df.OS you have put into the models are: BRCA1mutation BRCA2mutation BRCA1methylation, or: BRCA1mutation.StageII BRCA1mutation.StageIII and IV BRCA2mutation.StageII BRCA2mutation.StageIII and IV ...
written 22 months ago by liu4gre200
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Comment: C: cox proportional hazard model
... Thanks. But it looks the reference for each category can not be defined? E.g. Stage I as reference in Tumor stage and BRCA wildtype in BRCA status? Or in above table, the reference was defined individually, which means three testes were performed to generate the table of PFS or OS? ...
written 22 months ago by liu4gre200
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Comment: C: cox proportional hazard model
... Thanks, Kevin. It looks cool. But it is for univariable test? How about multivariable, e.g. BRCA status, Tumor stage and Residual tumor? ...
written 22 months ago by liu4gre200
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cox proportional hazard model
... Hi All, I am wondering how to derive HR, CI and p values for each factor from cox model like follows. Using coxph only gives these values for groups such as BRCA status, TUmor stage ... THanks. ![enter image description here][1] [1]: https://i.imgur.com/OepsUKo.png ...
cox survival written 22 months ago by liu4gre200 • updated 22 months ago by Kevin Blighe52k
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COSMIC paired normal cell lines for somatic mutation calling
... COSMIC used Caveman to call SNVs that requires both tumor and paired normal cell lines. My question is where the normal cell line from and where to find the data? Thanks. ...
dna-sequencing cosmic somatic mutation written 2.2 years ago by liu4gre200 • updated 2.0 years ago by Biostar ♦♦ 20
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where to get TCGA infiltrating lymphocyte data?
... Hi all, is there a place providing infiltrating lymphocyte for TCGA samples? Thanks. ...
tcga infiltrating lymphocyte written 2.6 years ago by liu4gre200
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how to correct gene expression based on tumor purity
... Hi all, I am looking at TCGA gene expression data. Also I am interested in tumor purity, which may be inferred by a few tools such as ABSOLUTE and ESTIMATE. Question is how to correct gene expression levels based on these inferred values? ...
gene expressin tumor purity absolut written 2.7 years ago by liu4gre200 • updated 14 months ago by Kevin Blighe52k
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Co-occurencing and mutually exclusive mutations
... how to use fisher's exact test to test if two genes have co-occurencing or mutatully exclusive mutations? ...
mutation written 2.7 years ago by liu4gre200
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Comment: C: tag density v.s. binding affinity v.s. signal value
... Great. Thanks a lot for the info. ...
written 5.0 years ago by liu4gre200

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For How To Annotate Methylation 450K?
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Popular Question 2.6 years ago, created a question with more than 1,000 views. For How To Annotate Methylation 450K?
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Popular Question 4.3 years ago, created a question with more than 1,000 views. For How To Calculate Maf From Tcga Data?
Popular Question 4.3 years ago, created a question with more than 1,000 views. For How To Annotate Methylation 450K?
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Popular Question 4.4 years ago, created a question with more than 1,000 views. For How To Annotate Methylation 450K?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For How To Annotate Methylation 450K?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For How To Annotate Methylation 450K?
Student 5.1 years ago, asked a question with at least 3 up-votes. For how to get TF binding affinity from ENCODE narrowPeak or broadPeak files?

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