change in expression patterns before and after marker re-naming (cyTOFKIT version 1.11.3)

CNicholasMDA commented 6 years ago

Hello Dr Chen and colleagues, I am enjoying the use of your cyTOFKIT program. Thank you for working so hard to make it user-friendly while executing various important clustering algorithms.

However, today I have encountered a problem and am not sure if it is user error or software error.

When I run the clustering algorithm and open the results in the shinyAPP viewer, I frequently like to re-name my protein markers and re-group my samples to rename them. However, I have noticed that after updating the marker names, the distribution of markers (CD3, for example) changes in the Marker Expression Level Plot. In addition, the expression pattern in the newly-assigned CD4 plot looks disturbingly similar to the “old” CD8a plot. This occurs regardless of whether I export a new RData file after updating the marker names.

Am I using a setting incorrectly, or is there a known software issue? (For now, I will be happy with not changing the marker names…)

image of CD3, CD4, and CD8a prior to marker re-naming:

image of CD3, CD4, and CD8a after marker re-naming:

Any suggestions you can offer are greatly appreciated.

CNicholasMDA commented 5 years ago

Additional information/feedback on my issue of Oct 2: I have detected that this bug also affects regrouping (renaming) of the Sample IDs. I began with an RData results file that contained 118 samples. After regrouping (modifying) the sample names, I only had 99 samples loaded in the GUI. There was no rhyme or reason to indicate why a particular subset of samples were dropped (no special characters, etc).

Any help or suggestions you have are greatly appreciated. Is it possible that I have a problem with a supporting package that is installed?

thank you, Courtney

xwxdazhong commented 5 years ago

Hi Courtney, I noticed the same thing when I used it and it is an interesting yet weird bug. not sure we will get a response on it.

traumenCapote commented 5 years ago

This is still an issue. Do not rename your markers.

jinmiaochen commented 5 years ago

Dear Users,

Thank you very much for your support and feedback. We will fix this bug by this week and update you.

Very sorry for slow reply. I will improve my communication on github forum. And many thanks to Sam who highlighted this issue to me.

Best, Jinmiao

jinmiaochen commented 5 years ago

Dear Users,

We have fixed this bug and updated on cytofkit2 at https://github.com/JinmiaoChenLab/cytofkit2

Please download and test it.

Thank you.

Best, Jinmiao

CNicholasMDA commented 5 years ago

Hi Dr Chen and team, Thank you. This is a great effort. We appreciate it. I do have one question - during this latest install (instructions in the abovementioned link for cytofkit2) I find that the program cannot find a package called cytofkit2. Which line of the installation instructions pertains to downloading and installing cytofkit2?

with thanks, Courtney

SamGG commented 5 years ago

Hi Courtney, The installation procedure is at https://github.com/JinmiaoChenLab/cytofkit2 in the scetion "Install this development version". Briefly:

if(!require(devtools)){
  install.packages("devtools") # If not already installed
}
devtools::install_github("JinmiaoChenLab/cytofkit2")

To use it:

library("cytofkit2")
cytofkit_shiny_dashboard()

JinmiaoChenLab / cytofkit

change in expression patterns before and after marker re-naming (cyTOFKIT version 1.11.3) #49