Dear Mario
When you point out that dot plots is a poor choice for presenting data
(single color dot plot), I was very surprised for that sentence. Then you
bring up that even color dot plots are not good, but contours are ok.
However, if you have a small population against a big one, when you use
contours you almost take out the small one and then your representation of
the small one will be at the best: one single contour. What about, when you
are using three or four colors and you will be interest in detection of
markers on this small population?
I put my point here, because I use to analyze Dendritic cells/Langerhans
cells that represent less than 1% of the PBMC and less than 1% of the skin
cells and may be 10 % of the cells in the lymph, with this little fraction
I should measured CD1a vs HLA-DR, and then selected and check for two other
markers. Then, my contour plot only shown an awfull spot that said nothing
to me and less to others that are not familiar with FACS. Actually, still
they do not buy that this spot were truly DC/LC.
Another point that I want to bring home is that if you put colors in your
graphics (dots, contours and histograms) in order to made them more reader
friendly, you should also be prepared to paid for that artistic feature and
in some journals it run as high as 1600 US dollars. I still have the letter
from some obscure middle man. Editors never get dirty on money. Even for
Swiss standards is very high. Therefore, I also propose, that if the figure
requires the color for better understanding, it should be always free. What
about open this can of worms, I guess we can propose this to the journals
that are publishing papers on cytometry
Rafael
>Alice laid the gauntlet at my feet, and now I will return the favor to all of
>those involved in this debate (or who wanted to be involved!). I will propose
>to Cytometry to write a perspective on the topic of FACS data display.
>Everyone
>now knows my bias against dot plots: I challenge any of those of you who
>champion dot plots (or even color dot plots) to join my effort and write a
>"counterpoint" analysis to provide a balancing viewpoint.
>
>This ongoing discussion has been most spirited and, I think, very informative.
>I think that we are winding down to repeating ourselves, so I will try to make
>this my last words to the mailing list, at least for now!
>
>Calman writes about dot plots:
>
>> Furthermore it stresses the single cell nature of the
>> data- each dot is a cell.
>
>No, no, no, no, no, no, no! This is precisely the problem! In dot plots,
>each
>dot can be one cell, two cells, three cells, or a thousand cells. You can
>never
>know which. This is the fundamental error of dot plots. Once again, the
>number
>of events you display in a dot plot can totally change how it appears--you are
>thereby inadvertently massaging the data.
>
>I agree with Alice that the precise way of contouring can affect how the more
>frequent populations appear. This is why the choice of contouring
>algorithms is
>so important! One of the most robust (in that it is objective, not allowing
>"user-defined" contouring levels, etc.) is probability contouring. This
>method
>of contouring has been adopted by SAS Institute for use in their bivariate
>displays--in addition, it is offered by several FACS data analysis packages.
>
>This method of contouring generates displays that are indepedent of the number
>of events collected -- something that no other display can do. Thus,
>using Dot
>plots or color dot plots or user-defined thresholding, I can make a variety of
>conclusions about the same sample depending solely on how many events I choose
>to collect (or display)!
>
>Jim Houston is 100% correct that the precise method of data display is
>critical.
>I urge reviewers and editors to demand that this information be included
>in all
>FACS data displays.
>
>Finally, one last word about "raw data." Let us not delude ourselves into
>thinking that dot plots or unsmoothed plots are "raw"--these themselves are
>presentations of highly processed data. Much more raw is the listmode
>data--why
>not publish tables of the basic values, then? (e.g., "Note how frequent
>are the
>events which have parameter 2 values between 1200 and 1240, and parameter 3
>values between 800 and 950. This suggests...")
>
>Of course, this is nonsense: but I bring it up to drive home the point that
>these displays are only called "raw" in order to subtly convey the mistaken
>impression that the original measurements haven't been tampered with. Of
>course, even the listmode data is only as raw as a well-done steak. There has
>been a lot of signal processing that converts the original photoelectron
>counts
>of the PMT into a computer stored value--there is averaging, smoothing,
>background correction, etc., etc.
>
>Once again, this brings us to the fundamental point of data display: to
>convey
>information accurately to the reader. I highly recommend a book by Edward
>Tufte, "The Visual Display of Quantitative Information," about this topic
>(especially to programmers developing analysis packages). This fabulous book
>shows how misleading different styles of graphs can be, and discusses some of
>the underlying principles of data display--principles largely ignored by
>developers of FACS data analysis programs.
>
>There was some discussion about art vs. science. Do not mistake artistry for
>disinformation! Of course there is art in science, and in the presentation of
>scientific data. If not, we would only see tables of numbers that would be
>incomprehensible--we are, after all, only human.
>
>mr
\|/
(o o)
________________________________oOo__(_)__oOo_________________________________
___/\_ | Rafael Nunez mailto:rafaeln@vetvir.unizh.ch
/ o \/| | University Inst.for Virology http://www.unizh.ch/vetvir
/ _| | Winterthurerstr. 266a Telephone: (+41) 1 6358710
/_/\__/-\/ | 8057 Zurich SWITZERLAND Faximile : (+41) 1 6358911
______________________________________________________________________________
This archive was generated by hypermail 2b29 : Wed Apr 03 2002 - 11:50:11 EST