User: Sirus
Sirus • 760
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Bioinformatics student
Posts by Sirus
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... @morovatunc , to avoid over-fitting, you can use all your data but by doing for example 10-fold cross-validation (the Caret package can do that for you). Then you'll get your variable importance.
Because theoretically, the signal that you'll find important is supposed to be important in any subse ...
written 11 weeks ago by
Sirus • 760
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... There are many ways in which you can do it.
Random forest are a good choice, after training you can look at the "variable importance" which will rank the variables of your model according to their contribution to the prediction.
You can check the section of [variable importance][1] section of the C ...
written 12 weeks ago by
Sirus • 760
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... It is much more different, bioconductor support is mainly to help with the questions related to bioconductor packages and R programming in bioinformatics, while Biostars is a general bioinformatics plateform. A new SE site similar to biostars will not bring any thing new. ...
written 3 months ago by
Sirus • 760
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... You can use the `findOverlapsOfPeaks` function from the [ChIPpeakAnno][1] package.
Just to make the code more easy to follow, I use the `readBroadPeak` function from the genomation package. But you don't need to use too many packages to do that.
Suppose you have 3 bed files in the boradPeak forma ...
written 4 months ago by
Sirus • 760
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... Are they from the same tumor or they are different ones ? ...
written 16 months ago by
Sirus • 760
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... Yeah,
A more elaborated model is in the jmosaics model
http://www.genomebiology.com/2013/14/4/R38
...
written 17 months ago by
Sirus • 760
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... For big networks visualization, I think R is not the best choice, you can save it in R as gml format of a ncol format (if you don't have attributes in your nodes) and visualize it in some specialized tools such as Gephi.
...
written 22 months ago by
Sirus • 760
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... Hi chenxiaoyu4,
The answer is 5 weeks after your post, but maybe it will be helpful for others.
The idea behind using two linkers is to estimate random interactions.
If you just use linker A and then do the mapping, you cannot know which interaction is real and which one is just a result of ran ...
written 2.6 years ago by
Sirus • 760
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... It seems there is a problem with the code (maybe was not updated by the authors)
I did the following changes in the `virtualArrayBuildfData` function, I remove the lines 62 and 63 :
rownames(exprs_z$data) <- exprs_z$labels[[1]][, 1]
colnames(exprs_z$data) <- exprs_z$labels[[2]][, 1]
exprs_z ...
written 2.7 years ago by
Sirus • 760
0
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... In my case I want the threshold to be dynamic for each mark, in this way I can annotate which parts are at the same time H3K4me1+, H3K4me3-,... etc
So I thought I can for each mark do the classification, and I can select any combination and just do the intersection. for the moment I am using the Poi ...
written 3.3 years ago by
Sirus • 760
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