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<p class="MsoNormal">Hi SCIF Cytometry Users,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’ll be hosting a high-dimensional data analysis workshop this Thursday, April 2 from 1PM-3PM on Zoom.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Here’s the meeting link: <a href="https://ucmerced.zoom.us/j/473177054">
https://ucmerced.zoom.us/j/473177054</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Also, tSNE is already built into FlowJo, but to use FlowSOM you’ll have to install a plugin. Here are the instructions for that:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><u>FlowSOM Installation:<o:p></o:p></u></b></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoListParagraphCxSpFirst" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1">
Make sure you have a recent version of FlowJo installed. Greater than 10.4.1 is required<o:p></o:p></li><ol style="margin-top:0in" start="1" type="a">
<li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level2 lfo1">
<a href="https://www.flowjo.com/solutions/flowjo/downloads">https://www.flowjo.com/solutions/flowjo/downloads</a><o:p></o:p></li></ol>
<li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1">
Install R to default location- <a href="https://www.r-project.org/">https://www.r-project.org/</a><o:p></o:p></li><li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1">
RStudio to default location - <a href="https://www.rstudio.com/products/rstudio/download/">
https://www.rstudio.com/products/rstudio/download/</a><o:p></o:p></li><li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1">
Download the FlowSOM plugin - <a href="https://exchange.flowjo.com/">https://exchange.flowjo.com/</a><o:p></o:p></li><ol style="margin-top:0in" start="1" type="a">
<li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level2 lfo1">
Unzip the folder to your desktop<o:p></o:p></li></ol>
<li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1">
Drag the FlowSOM_v2.6.jar file into the FlowJo plugin folder found in program files folder<o:p></o:p></li><ol style="margin-top:0in" start="1" type="a">
<li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level2 lfo1">
By default somewhere like: C:/program files/FlowJo V10/plugins<o:p></o:p></li></ol>
<li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1">
Open RStudio and use the following commands to install required packages:<o:p></o:p></li><ol style="margin-top:0in" start="1" type="a">
<li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level2 lfo1">
<span style="font-family:Menlo-Regular;color:#4D4D4D">source("<a href="https://bioconductor.org/biocLite.R">https://bioconductor.org/biocLite.R</a>")</span><o:p></o:p></li><li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level2 lfo1">
<span style="font-family:Menlo-Regular;color:#4D4D4D">biocLite("flowCore")</span><o:p></o:p></li><li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level2 lfo1">
<span style="font-family:Menlo-Regular;color:#4D4D4D">biocLite("FlowSOM")</span><o:p></o:p></li><li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level2 lfo1">
<span style="font-family:Menlo-Regular;color:#4D4D4D">install.packages("pheatmap")</span><o:p></o:p></li></ol>
<li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1">
Open FlowJo<o:p></o:p></li><li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1">
Go to FlowJo -> Preferences -> Diagnostics<o:p></o:p></li><li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1">
Under R path, browse to the folder where your R.exe file is located. <o:p></o:p></li><ol style="margin-top:0in" start="1" type="a">
<li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level2 lfo1">
For me the path was c:/program files/R/R-3.5.1/bin/<o:p></o:p></li></ol>
<li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1">
Click okay.<o:p></o:p></li><li class="MsoListParagraphCxSpMiddle" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1">
Restart Flowjo<o:p></o:p></li><li class="MsoListParagraphCxSpLast" style="margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1">
Click on Workspace -> Plugins<o:p></o:p></li></ol>
<p class="MsoNormal">Now tSNE and FlowSOM should both be listed<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#092F44;text-transform:uppercase">DAVID GRAVANO, PHD</span></b><span style="font-size:9.0pt;font-family:"Arial",sans-serif"><br>
<br>
</span><span style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#092F44;text-transform:uppercase">TECHNICAL DIRECTOR OF CYTOMETRY</span><span style="font-size:9.0pt;font-family:"Arial",sans-serif"><br>
</span><span style="font-size:7.5pt;font-family:"Arial",sans-serif;text-transform:uppercase">STEM CELL INSTRUMENTATION FOUNDRY</span><span style="font-size:9.0pt;font-family:"Arial",sans-serif"><br>
<span style="color:#999999">5200 Lake Road </span><span style="color:#DAAC00">|</span><span style="color:#999999"> Merced, California 95343<br>
tel. 209.228.4039 lab; 209.285.5726 mobile<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Arial",sans-serif"><a href="https://scif.ucmerced.edu/">https://scif.ucmerced.edu</a><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:8.5pt;font-family:"Arial",sans-serif;color:#EEEEEE;letter-spacing:1.9pt;background:#092F44">BUILDING THE FUTURE IN THE HEART OF CALIFORNIA</span></b><span style="font-size:9.0pt;font-family:"Arial",sans-serif"><o:p></o:p></span></p>
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