User: Mike
Mike • 1.3k
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Posts by Mike
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... Hi All,
I have TCGA MAF files and want to calculate base substitution mutation frequency (C>T , T>A , C>G , T>C , T>G , C>A) per sample. If anyone knows please help me ?
Thanks ...
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... Good list Kevin,
No. 6: Biostars.org's unsung heroes (Pierre Lindenbaum, Devon Ryan, Istvan Albert, genomax , Michael Dondrup , Kevin Blighe, WouterDeCoster, Alex Reynolds, Giovanni M Dall'Olio, Sean Davis , Emily_Ensembl etc)
...
written 10 weeks ago by
Mike • 1.3k
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... Thanks Kevin and bruce.moran for your help ...
written 11 weeks ago by
Mike • 1.3k
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... Thanks you so much Kevin, I also found a paper where they mentioned that..
> we calculated the TMB score as follows:
>
> total number of truncating mutations*1.5 + total number of non-truncating mutations*1.0.
Truncating mutations included nonsense, frame-shift deletion, frame-shift ...
written 11 weeks ago by
Mike • 1.3k
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... Thanks bruce.moran, I have TCGA MAF files (Mutation_Packager_Raw_Calls) downloaded from Broad Institute Firehose. ...
written 11 weeks ago by
Mike • 1.3k
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... Hi All,
What is difference between "Tumor Mutation Burden (TMB)" and "mutational load" ? I have mutation matrix for TCGA samples (generated from maftools, see below). I tried maftools and GenVisR but couldn't find any option to calculate TMB score. How can I calculate TMB score using mutation mat ...
written 11 weeks ago by
Mike • 1.3k
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... Thanks again, yes there is difference in HRs with confidence intervals (upper/lower 95)
HR HRlower HRupper
0.82 0.770 1.01 (discrete)
0.87 0.75 0.97 (continues)
...
written 4 months ago by
Mike • 1.3k
1
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... Thanks Kevin for your help, I found a relevant article on this issue.
Comparing continuous and discrete analyses of breast cancer survival information
https://www.sciencedirect.com/science/article/pii/S0888754316300684
...
written 4 months ago by
Mike • 1.3k
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... nearly the same results using Z-scores data for discrete (logrankP= 0.02 ) & continuous model (logrankP= 0.00004 ). ...
written 4 months ago by
Mike • 1.3k
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... Thanks Kevin, expression data is RSEM log2 and this is distribution.
https://ibb.co/pbWBV0g
Median expresssion values of this gene is 8.73 in 452 samples ...
written 4 months ago by
Mike • 1.3k
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For A: Protocol to Downlad TCGA data from GDC
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