User: Jack Luo

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Jack Luo340
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Posts by Jack Luo

<prev • 30 results • page 2 of 3 • next >
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Comment: C: question regarding using cummeRbund package
... Hi Val, Thanks. See below: > library(cummeRbund) > cuff <- readCufflinks(dir=system.file("extdata", package="cummeRbund")) > disp<-dispersionPlot(genes(cuff)) Error: could not find function "dispersionPlot" > dens<-csDensity(genes(cuff)) > densRep<-csDensity(genes(cuff), ...
written 5.4 years ago by Jack Luo340
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question regarding using cummeRbund package
... Hi Dan, Thanks for your email. Yeah, I installed the package using biocLite("cummeRbund"). There are some functions that work well, but not those functions I listed for error msg, not sure why. Thanks, -Jack On Fri, Jun 29, 2012 at 4:56 PM, Dan Tenenbaum wrote: > Hi Jack, > > On Fri, ...
written 5.4 years ago by Jack Luo340 • updated 5.4 years ago by Valerie Obenchain ♦♦ 6.4k
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question regarding using cummeRbund package
... Hi, I am a newbie to RNA-seq data and try to learn using the cummeRbund package. Some simple questions are: 1. My OS is windows 7. I have no problem installing the cummeRbund in R, but do I need to install cufflinks? I thought there is only linux and mac version of cufflinks, not windows. 2. When ...
cummerbund written 5.4 years ago by Jack Luo340 • updated 5.4 years ago by Dan Tenenbaum ♦♦ 8.2k
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Comment: C: what is the correct way of normalizing 3 different U133 platforms using RMA?
... Excellent, thanks a bunch! -Jack On Mon, Aug 15, 2011 at 3:16 PM, James W. MacDonald wrote: > An almost identical question was asked and answered today, so I would point > you to the archives: > > https://stat.ethz.ch/**pipermail/bioconductor/2011-**August/040726.h tml > > Best, ...
written 6.3 years ago by Jack Luo340
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what is the correct way of normalizing 3 different U133 platforms using RMA?
... I have a bunch of cel files profiled on U133A, U133A2 and U133plus2. Obviously, in order to combine them, I'll only focus on the common probes shared by the 3 different platforms. However, I am not sure what is the correct way of RMA normalizing them. Should cel files from the same platform RMA norm ...
probe written 6.3 years ago by Jack Luo340 • updated 6.3 years ago by James W. MacDonald45k
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Comment: C: stuck in biocLite("GEOquery")
... Hi Dan, Thanks for your reply. You are right that I am using windows and my OS is win7. Do you think the version of R might be a problem? I use 2.12.2 and the first sentence showing after I type biocLite("GEOquery") is: Using R version 2.12.2, biocinstall version 2.7.4. In addition, I am not clear ...
written 6.7 years ago by Jack Luo340
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stuck in biocLite("GEOquery")
... Hi, I am trying to use install GEOquery package in R and type: source("http://bioconductor.org/biocLite.R") biocLite("GEOquery") The sliding bar stops at some point, then I stopped the task and repeat it, then it stops in another place ..., but still not 100%. I keep doing this for many times and ...
geoquery written 6.7 years ago by Jack Luo340 • updated 6.7 years ago by Dan Tenenbaum ♦♦ 8.2k
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"No significant surrogate variables" for SVA (surrogate variable analysis)
... Hi, I am trying to learn how to use SVA. The example given in the bioconductor manual runs pretty smoothly with 1000 genes and 20 samples (10 in each group, genes 1-300 respond to the primary variable of interest, genes 200-500 respond to some other variable). However, if I change the matrix to eit ...
sva written 7.1 years ago by Jack Luo340
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error msg for probe match (altcdfenvs)
... Hi, I am new to the probe match package altcdfenvs, when I was trying the code from the link: http://127.0.0.1:21417/library/altcdfenvs/html/matchAffyProbes.html library(hgu133aprobe) filename <- system.file("exampleData", "sample.fasta", package="altcdfenvs") fasta.s ...
probe altcdfenvs written 7.1 years ago by Jack Luo340 • updated 7.1 years ago by Laurent Gautier2.2k
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Comment: C: question regarding differential expression
... Jim, Thanks for your detailed explanation on this, it's really helpful. I agree with you that the term "present/absent" might be problematic, perhaps a more accurate term is reliable/unreliable. I am not sure I agree that the technical and biological variability are completely confounded, it's well ...
written 7.2 years ago by Jack Luo340

Latest awards to Jack Luo

Student 3.7 years ago, asked a question with at least 3 up-votes. For conceptual question about FDR, FDR adjusted p-value and q-value
Great Question 3.7 years ago, created a question with more than 5,000 views. For conceptual question about FDR, FDR adjusted p-value and q-value
Epic Question 3.7 years ago, created a question with more than 10,000 views. For conceptual question about FDR, FDR adjusted p-value and q-value
Popular Question 3.7 years ago, created a question with more than 1,000 views. For conceptual question about FDR, FDR adjusted p-value and q-value
Popular Question 3.7 years ago, created a question with more than 1,000 views. For conceptual question about FDR, FDR adjusted p-value and q-value

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