User: haiying.kong

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haiying.kong220
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Germany
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2 months, 4 weeks ago
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Posts by haiying.kong

<prev • 119 results • page 1 of 12 • next >
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5 follow
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KEGGREST -- gene list
... library(KEGGREST) > names(keggGet("map07049")[[1]]) [1] "ENTRY" "NAME" "PATHWAY_MAP" "COMPOUND" "REFERENCE" I need to get gene list (hugo-symbol) in each pathway. How can I get this from KEGGREST? > sessionInfo() R version 3.3.3 (2017-03-06) Platf ...
R keggrest bioconductor written 3 months ago by haiying.kong220 • updated 12 weeks ago by Damian Kao14k
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Comment: C: Do structural variations on pseudo-gene mean any thing?
... Thank you very much for your reply. I have whole exome sequence data from matched blood and tumor samples, used Mirkat to identify somatic structural variations, then annotated them with gene names. ...
written 3 months ago by haiying.kong220
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Do structural variations on pseudo-gene mean any thing?
... I found structural variations from WES data. The top frequency genes are almost all pseudogenes. Could anyone please give me any advice? ...
biology written 3 months ago by haiying.kong220 • updated 3 months ago by d-cameron1.8k
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Comment: C: R survivalsvm package
... Not really. It is a general question about the software tool. For instance, if I run the example code on the manual of the software, the predicted values are: > pred.survsvm.reg$predicted [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [1,] 13.88731 14.94699 11.12112 ...
written 3 months ago by haiying.kong220
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R survivalsvm package
... Dear All, I am trying to use the R package: survivalsvm. I can get it running without error, survivalsvm and predict.survival, but if I look at the predicted values from the output of predict.survivalsvm, the values are not easy to interpret. They did not look like expected relapse time, or pro ...
R written 3 months ago by haiying.kong220
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Comment: C: I am asked to run MutSigCV on sample size 2!!!!!!
... Then, he will say: You are making excuse to be lazy! ...
written 5 months ago by haiying.kong220
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Comment: C: I am asked to run MutSigCV on sample size 2!!!!!!
... Thanks for the advice. If I run, there will be no driver genes identified. So nothing can be included in any paper that can be published. Just waste of my time. But I will keep the email anyway. ...
written 5 months ago by haiying.kong220
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Comment: C: I am asked to run MutSigCV on sample size 2!!!!!!
... Such communication is impossible with such dense head, sorry to say this word. After "because", there will be scientific explanation that involves statistics, and he refuses to hear any bioinformatics, or statistics, or mathematics in any occasion. He is 100000% pure biologist. ...
written 5 months ago by haiying.kong220
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Is epigenetic still hot field?
... It was very hot several years back. Is it still hot field? I feel much is done in this field, and nothing original is coming out. ...
epigenetic written 5 months ago by haiying.kong220 • updated 5 months ago by Devon Ryan81k
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Comment: C: WES -- How come I found 40% mutations intron regions
... Thanks again for your help. It takes very very long to run MuTect even with many cores or nodes. So I do not have time to rerun, because I am trying to finish up soon. Is there any way to do the filtering from MuTect output? ...
written 6 months ago by haiying.kong220

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