User: Yue Li

gravatar for Yue Li
Yue Li370
Reputation:
370
Status:
Trusted
Location:
USA
Website:
http://people.csail.mi...
Last seen:
3 years, 9 months ago
Joined:
7 years, 6 months ago
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Posts by Yue Li

<prev • 36 results • page 1 of 4 • next >
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Answer: A: an annotation error when using RIPSeeker
... Hi, Thanks for reporting the error. Sorry for the late response. Indeed, I'm getting the same error. There seems to be an issue on the Ensembl database query for the archived database. My package relies on annotatePeakInBatch {ChIPpeakAnno}, which itself relies on useMart {biomaRt}. I got the same ...
written 3.8 years ago by Yue Li370
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Answer: A: Algorithm description for matchPWM (Biostrings)
... Hi Herve, Thanks a lot for the quick reply. Since the cutoff is defined as percentage, the actual score for a subsequence is just the sum of the scores corresponding to each nucleotide in that sequence divided by maximum of the total scores (for an optimal subsequence)? Thanks, Yue   ...
written 5.2 years ago by Yue Li370
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Algorithm description for matchPWM (Biostrings)
... Dear List, I wonder if you could kindly point me to a clear description of the algorithm that matchPWM implementation is based on, preferably a peer-reviewed publication. I apologize in advance for not being able to see the obvious answer here. But the reference (Wasserman and Sandelin, 2004 Nat. ...
biostrings matchpwm written 5.2 years ago by Yue Li370 • updated 5.2 years ago by Hervé Pagès ♦♦ 14k
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Comment: C: fail to load BSgenome.Hsapiens.UCSC.hg19
... Hi Herv?, Thanks a lot! I actually went the brute force way by restoring my whole library via time machine backup. I will try my luck again tomorrow. Best, Yue On May 6, 2014, at 3:47 PM, Hervé Pagès wrote: > Hi Yue, > > Please ask Bioc-devel questions on the Bioc-devel mailing list. ...
written 5.5 years ago by Yue Li370
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fail to load BSgenome.Hsapiens.UCSC.hg19
... Dear List, I am experiencing the following problem after I updated some of the packages today and wonder if there's a quick fix for it. Thanks in advance! Yue ################################################################ R version 3.1.0 Patched (2014-04-15 r65398) -- "Spring Dance" Copyright ...
written 5.5 years ago by Yue Li370 • updated 5.5 years ago by Hervé Pagès ♦♦ 14k
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Fontconfig error in R 3.10 when running
... Dear List, After updating to R 3.10 and Bioconductor 2.14, I'm having a rather frustrating error whenever I try using function like cairo_ps to save eps figures as demonstrated in the following example: cairo_ps('test.eps') plot(c(1:10),c(1:10)) Fontconfig error: Cannot load default config file de ...
written 5.6 years ago by Yue Li370 • updated 5.6 years ago by Vincent J. Carey, Jr.6.3k
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Comment: C: plotMA {limma} wrong xlab - a bug?
... Apparently limma_3.18.13 fixed the bug! Thanks again. On Mar 28, 2014, at 4:54 PM, Yue Li wrote: > Thanks Jim. I am upgrading all of my installed bioc packages. It's likely to just be the transient bug from the old version of limma package like you mentioned. > > > On Mar 28, 2014, a ...
written 5.6 years ago by Yue Li370
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Comment: C: plotMA {limma} wrong xlab - a bug?
... Thanks Jim. I am upgrading all of my installed bioc packages. It's likely to just be the transient bug from the old version of limma package like you mentioned. On Mar 28, 2014, at 4:51 PM, James W. MacDonald wrote: > Hi Yue, > > Here is what I get: > > > library(limma) > &g ...
written 5.6 years ago by Yue Li370
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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 5.6 years ago by Yue Li370
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plotMA {limma} wrong xlab - a bug?
... Dear List, Somehow the plotMA function in limma package labels both x and y-axis title as 'M', where x-axis title should have been "A". The function resist the changes I try to make by setting the xlab in the plotMA function. See example below. I wonder if anyone came across the same thing and fo ...
limma written 5.6 years ago by Yue Li370 • updated 5.6 years ago by James W. MacDonald51k

Latest awards to Yue Li

Popular Question 3.7 years ago, created a question with more than 1,000 views. For fail to load BSgenome.Hsapiens.UCSC.hg19
Popular Question 3.7 years ago, created a question with more than 1,000 views. For how to build a R package with the inclusion of inst/extdata
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Algorithm description for matchPWM (Biostrings)
Popular Question 3.7 years ago, created a question with more than 1,000 views. For lower.limits and upper.limits in glmnet
Student 3.7 years ago, asked a question with at least 3 up-votes. For Algorithm description for matchPWM (Biostrings)
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Algorithm description for matchPWM (Biostrings)

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