when I run Citrus in R, why there is "clustering parameters: None Selected"? How to fix it? Thanks a lot.

[liyan99]

[rbruggner]

You must assign samples to groups before you can select clustering parameters.

[liyan99]

I have assign samples later, but it still showed the same, it seemed there is no parameters I can select? Is there any other reason for this? Thanks a lot.

[rbruggner]

Can you post a screenshot of the "clustering setup" tab?

On Oct 30, 2016, at 9:43 PM, liyan99 [email protected] wrote:

I have assign samples later, but it still showed the same, it seemed there is no parameters I can select? Is there any other reason for this? Thanks a lot.

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[liyan99]

[liyan99]

There is parameters for me to select. Thanks a lot.

[rbruggner]

You must assign samples to groups (in the "Sample group setup" tab) before you can select clustering parameters.

See the instructions here:
https://github.com/nolanlab/citrus/wiki/Getting-Started#Specifying_an_experimental_endpoint

[liyan99]

[liyan99]

[liyan99]

I have assigned samples to groups, but it still did not work out.

[rbruggner]

This could be a bug, but one more thing to check: In order for parameters to show up in the "clustering setup" tab, they must appear in all files, be measured on the same channel, and be named the exact same thing (including capitalization).

Can you upload the content of the R console after you run the citrus.launchUI() function? Please include everything up to the line Listening on http://127.0.0.1:7247.

It should have a bunch of lines talking about reading parameters from files.

[liyan99]

[liyan99]

I have change to another set of samples, it still showed the same.

[liyan99]

what is the difference between "127.0.0.1:7247". and "127.0.0.1:4692"?

[liyan99]

I am going to restart my computer to see if it works. Thanks a lot.

[liyan99]

I have restarted my computer, it is still the same. Is there any way to fix it? Thanks a lot.

[JimboMahoney]

Just to report that I see the same issue.

UPDATE - Actually, I ran it again, including loading some other packages and now it works.

My guess is that I (and @liyan99) was previously using simply this:

library("citrus")
citrus.launchUI()

Here's the code I used:

if (!require("devtools")) {
  install.packages("devtools", dependencies = TRUE)
  library(devtools)
}

if (!require("Rclusterpp")) {
  install_github("nolanlab/Rclusterpp",dependencies = TRUE)
  library(Rclusterpp)
}

if (!require("impute")) {
  if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
  
  BiocManager::install("impute")
}

if (!require("citrus")) {
  install_github("nolanlab/citrus",dependencies = TRUE)
  library(citrus)
}

citrus.launchUI()

[SamGG]

Hi James,
Sounds like your code is an update of the installation process given at https://github.com/nolanlab/citrus/wiki/Installing-Citrus#citrus-package-prerequisites-installation and https://github.com/nolanlab/citrus/wiki/Installing-Citrus#standard-citrus-installation-no-openmp-support. Both those sections are needed before running citrus in my experience.
Once installation is done successfully once, the two lines of codes should be sufficient (double quote are not needed in the library call on the contrary to the installation call).

library(citrus)
citrus.launchUI()

Best.

[JimboMahoney]

Thanks - agreed.

Re: Double quotes - that's just a straight copy/paste from https://github.com/nolanlab/citrus/wiki/Installing-Citrus#standard-citrus-installation-no-openmp-support - I'm not using it myself.