User: Yue Li

gravatar for Yue Li
Yue Li60
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5 years, 8 months ago
Joined:
7 years, 7 months ago
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y****@cs.toronto.edu

Posts by Yue Li

<prev • 6 results • page 1 of 1 • next >
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Comment: C: plotMA {limma} wrong xlab - a bug?
... Hi Jim, I tried it on both my Mac and Linux server and observed the same outcomes. Here are the session info. Mac: R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats ...
written 5.7 years ago by Yue Li60
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Comment: C: lower.limits and upper.limits in glmnet
... Hi Steve, Thanks for the reply. Yes, I tried it and it does seem to do that. I was just uncertain about how is achieved. Thanks anyways. Input: mycoef1 <- as.matrix(coef(glmnet(x,y,alpha=1,intercept=F),s=0.01)) mycoef2 <- as.matrix(coef(glmnet(x,y,alpha=1,intercept=F,upper.limits= c(rep(Inf ...
written 6.1 years ago by Yue Li60
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Answer: A: lower.limits and upper.limits in glmnet
... Dear List, A quick question about using the glmnet package (which I know is not a BioC package ... apologies): Would the options "upper.limits" and "lower.limits" in glmnet be equivalent to an additionally constrained optimization on the range of the coefficients? For instance, would setting uppe ...
written 6.1 years ago by Yue Li60
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Comment: C: RIPSeeker multicore option not working fully?
... Hi Wade, As Dan mentioned, that's most likely the cost. Other than that, it would be able to use however many cores you have on the machine when multicore set TRUE. Thanks Dan. Yue On 2013-07-31, at 4:51 PM, Dan Tenenbaum wrote: > On Wed, Jul 31, 2013 at 1:28 PM, Davis, Wade > wrote: &g ...
written 6.3 years ago by Yue Li60
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Answer: A: submission of new package
... Dear Bioconductor colleagues, I have a question regarding to the new package submission associated with a peer-review manuscript to some journal. The way I understand is that I first submit my package to Dr. Marc Carlson for review. Meanwhile, I could submit my manuscript describing the algorithm ...
written 7.2 years ago by Yue Li60
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Answer: A: problem with loading DESeq after upgrading from R 2.14 to R 2.15
... Dear List, I have some problem loading DESeq after I upgraded from R 2.14 to R .2.15 on Mac OS 10.7.3. Basically, I have my own library directory separate from the default library directory (/Library/Frameworks/R.framework/Versions/2.14/Resources/library) to avoid having to re-instally all the pac ...
written 7.6 years ago by Yue Li60

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