The Daily Dongle

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experienced flowjo users are well aware of a problem in flowjo, where a moved worksapce will lose data link to the FCS files if the file names were too long. My advice is to truncate file names. This advice comes in "free" and "awesome" flavors. hint: modifying original files can... Read more →

OS X leopard

I got my copy of Leopard on Friday. I had a chance to run the basic 4x4 benchmark (publicly available, email me for a link and instructions) on the same computer before/after the upgrade. The performance appears unchanged, with exception of RAMdisk times, which I will need to re-test on... Read more →

mac version and biexponential transforms

There are two preferences and one user action involved in setting biexponential scaling in FJ Mac. First, there is the "enable transformation" preference, which is buried in FlowJo>> Preferences >> workspace tab >> define.. button >>. This preference controls whether or not there will be negative events. Second, there is... Read more →

Create Translucent Graphs Like FlowJo's Home Page

When you create a Histogram Overlay in FlowJo's Layout Editor, you can display the histograms with a translucent color, rendering the plot easier to read and/or sexier. Histogram transparency is available in FlowJo for PC if you right-click on the sample name in the legend and select Coloring -> Tinted.... Read more →

FlowJo keywords thread on Purdue

In response to users' questions about keywords and FlowJo, I've created some additional documentation regarding keyword handling. This is presented in three and a half parts: 1. review (applies to both Mac and PC versions) these are mac-version specific: 2. keyword migration from one flowjo workspace to another, also from... Read more →

Mean, Median, Mode.

Many novice users call and ask us about 'mfi' of their data. Since the acronym is ambiguous, we ask the scientist to specify if they are asking about median, mean, or geometric mean fluorescence intensity. Mean and Geometric mean are easiest to understand - here are their formulae (from wikipedia):... Read more →

FlowJo templates part 2

Last time, we covered a linear template - where all tubes get the same gating treatment. This time, we'll focus on sequential templates. A sequential template is meant for experiments with "panels" - ie. each "patient" gets a certain amount of "tubes" each of which has some specific reagent combination.... Read more →

FlowJo's tables formatting in excel

Some users commented that flowjo V7's clipboard output of the table editor is too formatted. Workarounds: save your tables in excel (XLS) format. save your tables in csv format and import into another spreadsheet. copy/paste the formatted values to excel. Then, copy them again from excel, and paste-special-values-only eslewhere in... Read more →

FMO vs. compensation

From tech support file - how should I use my FMO tube to define "negative" cells for fluorescence compensation ? There are two different concepts of negativity we need to differentiate. An FMO control helps you to quantify the contribution of your combination of reagents to a specific channel where... Read more →

FlowJo templates part 1

This week I'll be documenting template creation logic. This process relies heavily on metadata, which is why I documented keywords last week. Definition: A template is a special FlowJo workspace which contains the analyses but not the samples. It is intended to be reused for analyzing data analogous to the... Read more →