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How is the collective going to select theĮxperts?Surely the people who are publishing this stuff ARE peopleīoards is probably going to end up in a status quo. nowDoYouSee.gif (Who's computer is this?) Oh, alright then, I've put a further figure up with two dot plots and twoĬontour plots with paired numbers of events at: On the plot than numbering the events on the two contour plots (upper left The dot plot of 1600 cells (not shown for brevity) clearly has fewerĬells than that of 10000, and does a better job of warning the viewer,Įxpert or not, of how confident they should be in making conclusions based Would labelling the upper left and lower left plots as having the same number of cells be enough to make you see them as representing the exact same data What's an expert to do when presented with this kind of thing? The smoothing belies the sparsity of the data. The lower right plot shows a density plot from FlowJo,
FLOWJO 10 MAKE HISTOGRAMS MATCH FULL SIZE
Shows this graph at full size with no dithering) You'll notice that using higher resolution avoids much of the coalescing to a black blob that you object to in dot plots (and does) print on a printer which isn't limited to screen resolution (the data has a range of 512 "channels"),įCSPress has dithered the plot to represent how it would The lower central plot is a dot plot from FCSPress, plotting data at 512 points along the axis The lower left plot is a log 50% contour plot of the data in the top leftĪnd top centre plots, what is one to make of those contours based on four Shows the crowding you object to, the upper central plot is FlowJo's default contour plot of SSCvFSC with ten thousandĬells, the upper right plot is a plot of 1600 cells gated from the same (the data is from the FlowJo tutorial set, the figures are made in FlowJo 3.2 and FCSPress 1.3). I've restrained myself, and made them available at:į/512AlongTheAxis.gif (Who's computer is this?)įcspress.gif (Who's computer is this?) > shows how strikingly different contour plots of the same data can be I'm sorely tempted to attach a few figures to this e-mail, Them?", and suggest that contour plots need even more annotation. Reverse your logic in " remember that contour plots are alsoĬorresponding to event frequency. I'm going to take you back a few years to ourĭiscussion on dot plot versus contour, and how misleading contours are. Subject: Re: Bad Flow Data & reviewing - What can we do? We'll provide more info as it becomes available.
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We will try to provide filled out examples for each of the instruments so that you can simply modify them for your use. If you have any questions, or need help filling in the appropriate information, the flow can certainly help. has decided to adopt them sooner rather than later, but we anticipate more and more journals will begin to require this information. These are a few of the guidelines that will be implemented soon. For example, did you draw them based on unstained cells, or an isotype control, or and FMO control, or did you just subjectively draw it around a population. You must also state how you drew your gates. This can (and probably should) be in the supplemental data portion of the manuscript. Back-gating analysis is the best way to show this. You MUST show the entire gating tree for your figure as an example. Graph-types should be used consistently throughout. The frequency of populations must be displayed on the plot or in a table The number of events in a plot must be displayed in the plot or figure legend. Med.Īxis on plots must have the reagent and fluorescence labelled (ex. This will be done in an excel template that will be available from ISAC or J. Once a comprehensive list is created, I'll post them for the group to see.Īuthor must list the instrument(s) used, the laser(s) used for excitation, and the filter(s) used for emission. Here are a few examples from the guidelines.
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Mario Roederer, shared the conclusions of the committee this week at the ISAC Congress. A member of the Data Standards Committee, Dr. Being the premier flow cytometry authority, ISAC has taken it upon itself to lay down some guidelines to assist authors in properly presenting the necessary information to describe their flow cytometric data. It's not that the data is bad, or doesn't support the authors conclusions, it's just that the figure is annotated so poorly, and the methods written so vaguely that it's nearly impossible for anyone to try and repeat complicated analyses. What the cytometry field has been noticing for quite a while is the amount of publications in high-end journals with really poor flow cytometry figures. anytime soon? Well then you'll want to pay attention to the new guidelines generated by the Data Presentation Standards Committee and adopted by J.