[SCIF Flow Cytometry] SCIF Cytometry Data Workshop - Thursday 1PM on Zoom

[David Gravano]

Hi SCIF Cytometry Users,

I'll be hosting a high-dimensional data analysis workshop this Thursday, April 2 from 1PM-3PM on Zoom.

Here's the meeting link: https://ucmerced.zoom.us/j/473177054

I'll be sharing my screen and using FlowJo tools. However, tSNE and FlowSOM can be used with other analysis platforms such as R or FCSExpress. In the workshop I'll present a how-to on visualizing high dimensional data with tSNE, creating clusters with FlowSOM, and comparing those clusters across samples. This is especially relevant to those of you using 8+ colors in your experiments and these tools are some of the most widely used ones for high-dimensional flow analysis.

All are welcome to attend and observe. If you want to perform the analysis in parallel, I'll have the relevant files in a Box folder that will be shared with meeting participants. You will need FlowJo version 10.4 or greater. I would recommend downloading version 10.6 as the speed of these algorithms has improved in newer versions.

Also, tSNE is already built into FlowJo, but to use FlowSOM you'll have to install a plugin. Here are the instructions for that:

FlowSOM Installation:

  1.  Make sure you have a recent version of FlowJo installed. Greater than 10.4.1 is required
     *   https://www.flowjo.com/solutions/flowjo/downloads
  2.  Install R to default location- https://www.r-project.org/
  3.  RStudio to default location - https://www.rstudio.com/products/rstudio/download/
  4.  Download the FlowSOM plugin - https://exchange.flowjo.com/
     *   Unzip the folder to your desktop
  5.  Drag the FlowSOM_v2.6.jar file into the FlowJo plugin folder found in program files folder
     *   By default somewhere like: C:/program files/FlowJo V10/plugins
  6.  Open RStudio and use the following commands to install required packages:
     *   source("https://bioconductor.org/biocLite.R")
     *   biocLite("flowCore")
     *   biocLite("FlowSOM")
     *   install.packages("pheatmap")
  7.  Open FlowJo
  8.  Go to FlowJo -> Preferences -> Diagnostics
  9.  Under R path, browse to the folder where your R.exe file is located.
     *   For me the path was c:/program files/R/R-3.5.1/bin/
  10. Click okay.
  11. Restart Flowjo
  12. Click on Workspace -> Plugins
Now tSNE and FlowSOM should both be listed

[cid:image001.png at 01D60681.A127B450]
DAVID GRAVANO, PHD

TECHNICAL DIRECTOR OF CYTOMETRY
STEM CELL INSTRUMENTATION FOUNDRY
5200 Lake Road | Merced, California 95343
tel. 209.228.4039 lab; 209.285.5726 mobile
https://scif.ucmerced.edu<https://scif.ucmerced.edu/>
BUILDING THE FUTURE IN THE HEART OF CALIFORNIA


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.ucmerced.edu/pipermail/scifflowcytometry/attachments/20200330/70efb048/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 9677 bytes
Desc: image001.png
URL: <http://lists.ucmerced.edu/pipermail/scifflowcytometry/attachments/20200330/70efb048/attachment-0001.png>