User: jdangelo

gravatar for jdangelo
jdangelo0
Reputation:
0
Status:
New User
Location:
United States
Last seen:
1 year, 10 months ago
Joined:
2 years, 1 month ago
Email:
j*******@ucsd.edu

Posts by jdangelo

<prev • 11 results • page 1 of 2 • next >
0
votes
0
answers
425
views
0
answers
ChAMP: Error using champ.norm() function
... Hello,  I am currently trying to use the ChAMP package in R on a set of 60 samples and have run into a problem with the champ.norm() function.  I am using ChAMP version 1.4.1 and 64-bit R version 3.1.2 and am using a cluster with 16GB of RAM.  The error, when running champ.norm() is: Error in de ...
epigenetics champ methylation written 2.1 years ago by jdangelo0
0
votes
1
answer
764
views
1
answer
ChAMP error: "Error in density.default(beta1.v[class1.v == 1]) :need at least 2 points to select a bandwidth automatically..."
... Hello,  I am currently trying to use the ChAMP Bioconductor package to process my methylation data. Here is my sessionInfo(): R version 3.1.2 (2014-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit)  attached base packages: [1] stats4    parallel  stats     graphics  grDevices utils     dataset ...
champ written 2.1 years ago by jdangelo0 • updated 15 months ago by rl13850
1
vote
1
answer
596
views
1
answer
Trouble understanding how to load my idat files into MethylAid.
... Hello, I am currently trying to use the MethylAid package to visualize methylation array data in the form of idat files. My directory of files contains the idat, jpg, locs and xml files. I am trying to follow the tutorial from https://www.bioconductor.org/packages/release/bioc/vignettes/MethylAid/i ...
methylaid written 2.1 years ago by jdangelo0 • updated 2.1 years ago by m.van_iterson20
0
votes
1
answers
510
views
1
answers
Comment: C: MethylAid package visualize function not opening a web browser
... Sorry for the late update, but in the end I was not able to get a port opened from support because of security issues (working through a hospital network server). What I ended up doing was to install RStudio on my local machine and install methylaid onto the local machine. Then I had to copy whateve ...
written 2.1 years ago by jdangelo0
0
votes
1
answers
510
views
1
answers
Comment: C: MethylAid package visualize function not opening a web browser
... To my understanding, VMWare is run as a hosted application through the local computer. I don't really know if it is a "guest" on my machine, but if it helps, I can access the mounted drive that is on the VM through my desktop. I also know that I have to use a vpn to connect to the school server befo ...
written 2.1 years ago by jdangelo0
0
votes
1
answers
510
views
1
answers
Comment: C: MethylAid package visualize function not opening a web browser
... I used a VMware VM and connect to it through ssh with the VM's IP address through putty.  Sorry I took so long to answer, my rating only allows a few posts every 6 hours. Do you have any other suggestions? Thanks again, Julian ...
written 2.1 years ago by jdangelo0
0
votes
1
answers
510
views
1
answers
Answer: A: MethylAid package visualize function not opening a web browser
... Sorry for the confusion, but I did NOT use 1.2.3.4 as the VM's IP. I used my actual VM's IP address.      ...
written 2.1 years ago by jdangelo0
0
votes
1
answers
510
views
1
answers
Comment: C: MethylAid package visualize function not opening a web browser
... Thanks for the quick response again=) I tried your solution and change shiny.host to my VM's IP address and re-ran the visualize command. However, when I ran it, I got the following error: Listening on http://1.2.3.4:XXXX Error in startServer(host, port, handlerManager$createHttpuvApp()) :   Fail ...
written 2.1 years ago by jdangelo0
0
votes
1
answers
510
views
1
answers
Comment: C: MethylAid package visualize function not opening a web browser
... Thank you for the response Dan, What you are saying about running R on a different machine is definitely the case. I am running R through the terminal which is connected to a VM and I am trying to open us the web browser on my local computer. I did indeed try to open up a web browser and use the U ...
written 2.1 years ago by jdangelo0
0
votes
1
answers
510
views
1
answers
Comment: C: MethylAid package visualize function not opening a web browser
... More info on my issue: The response to calling visualize(data) is the output: The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1) The 'clickId' argument is deprecated.  Please use 'click' instead.   ...
written 2.1 years ago by jdangelo0

Latest awards to jdangelo

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 175 users visited in the last hour