To add one more point to the counts per channel discussion:
As with FCSPress, CellQuest will give you counts per channel directly.
If you move the cursor over a histogram which displays only one data set,
you will see the numbers changing in the boxes labeled "X" and "Y" in the
upper left corner of the CellQuest document. The X coordinate represents
either the linear value or the channel value (you choose this under the
Plots menu: Log Data Units...). The Y coordinate shows the count for that
channel. Values for X and Y are not displayed if you have more than one
data set per histogram. On a dot plot X and Y refer to channel numbers and
not to counts in that box. Clearly this is only useful if you want a few
particular channels values and not the counts across the whole histogram.
I have a separate question: "After-the-fact compensation"
We have numerous FCS files (generated on a Coulter Elite using Expo
software but typically analyzed using CellQuest). We would like to try
different kinds of compensation, after the experiment is over. The object
is primarily to remove autofluorescence in order to improve the signal to
noise ratio of our samples. In other words we would like to run "induced"
and uninduced" samples at various voltage settings for the different PMTs
and, at a later point, try correcting for autofluorescence by subtracting a
fraction of one channel from another channel.
Ideally this would be a program which inputs one or more FCS files
together with an algebraic expression representing the operation to be done
on the files and outputs FCS files containing the altered parameter (or
maybe a new parameter representing the transformed data). The only trick
might be that log data would have to be converted to a linear signal before
subtraction and then converted back to log data.
Mark Poritz, Ph.D.
Senior Scientist
Arcaris Inc.
615 Arapeen Dr., Suite 300
Salt Lake City, UT 84108
801-303-0300, 0333 fax
(formerly Ventana Genetics)
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