User: remy.c.nicolle

Reputation:
10
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New User
Location:
CIT, Ligue Nationale Contre le Cancer, Paris, France
Last seen:
2 years, 2 months ago
Joined:
5 years, 1 month ago
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r*************@gmail.com

Posts by remy.c.nicolle

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Error in referencecn.mops() for paired exome sequencing (normal/tumor)
... Dear Günther, I managed to solve my problem. So, I happen to load the "scales" package from the CRAN (I'm not even sure why, but I do by default) and this package happens to have a function called alpha. Now at line 462 of the referencecn.mops, the function tests wether alpha is set and if not sets ...
written 3.8 years ago by remy.c.nicolle10
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Answer: A: Error in referencecn.mops() for paired exome sequencing (normal/tumor)
... Thanks for your reply Günther. I used getReadCountsFromBAM instead of getSegmentReadCountsFromBAM. I checked the two matrices and all samples have more than 4M counts. I removed every line in the matrices that had a zero value for all samples, about 4K lines in 50K total and I still got the same ...
written 3.8 years ago by remy.c.nicolle10
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Error in referencecn.mops() for paired exome sequencing (normal/tumor)
... I used getSegmentReadCountsFromBAM() to get a GRanges object from a list of tumor-normal bam files Then I used referencecn.mops() which triggered the following (french) error :   NOTE: The default parameters are adjusted for "tumor-vs-normal"! Normalizing... Starting local modeling, please be pa ...
cn.mops written 3.9 years ago by remy.c.nicolle10 • updated 3.8 years ago by Günter Klambauer540
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Comment: C: Problem with hLICORN function of CoRegNet
... Yes, that's exactly what I was going to suggest until I realised my reputation is so bad around here that I couldn't do anything anymore and certainly not try to help you using my own package. Anyway, the next possible fix is to try again (try all the tests I proposed here in reverse chronological ...
written 4.3 years ago by remy.c.nicolle10
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Comment: C: Problem with hLICORN function of CoRegNet
... This is crazy, your version of arules doesn't work. Now, aside from reinstalling it, I do not see what else you could do. install.packages("arules") and try again the last bit, (including the library(arules) )   ...
written 4.3 years ago by remy.c.nicolle10
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Comment: C: Problem with hLICORN function of CoRegNet
... OK. The problem clearly comes from the arules package. I'll let you try something I directly got out of the package help : library(arules) a_matrix <- matrix( c(1,1,1,0,0, 1,1,0,0,0, 1,1,0,1,0, 0,0,1,0,1, 1,1,0,1,1), ncol = 5) ## set dim names dimnames(a_matrix) <-  list( c("a","b", ...
written 4.3 years ago by remy.c.nicolle10
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Comment: C: Problem with hLICORN function of CoRegNet
... Well, something is going wrong with your version of arules or of Matrix. I'm soory to make you try so many things but I'd really like to track down your error.   Would you mind trying this ?   gexp=matrix(rnorm(2600,sd=3),ncol=100) gexp=rbind(gexp,do.call(rbind,lapply(1:26,function(i){ tf = s ...
written 4.3 years ago by remy.c.nicolle10
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Comment: C: Problem with hLICORN function of CoRegNet
... Try loading the parallel package beforehand (library(parallel)) and run hLICORN with the verbose parameter to TRUE :   library(parallel) gexp=matrix(rnorm(2600,sd=3),ncol=100) gexp=rbind(gexp,do.call(rbind,lapply(1:26,function(i){ tf = sample(1:26,4) return((gexp[tf[1],]+gexp[tf[2],] -gexp[tf[ ...
written 4.3 years ago by remy.c.nicolle10
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Answer: A: Problem with hLICORN function of CoRegNet
... Hi Aaerp, I'm sorry you're experiencing some problems with the package. Unfortunately, I'm absolutely unable to reproduce your errors. I do get some warnings (that I should correct anyhow) but a it works find on the machines I tested.  I'll try to look deeper in the code but for now, you may want ...
written 4.3 years ago by remy.c.nicolle10

Latest awards to remy.c.nicolle

Scholar 3.8 years ago, created an answer that has been accepted. For A: Error in referencecn.mops() for paired exome sequencing (normal/tumor)

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