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Heat 3358: export data for several profiles/experiments using Trend Viewer
Judith Boer <j.m.boer@lumc.nl>
2003-03-03 12:05:19
Hi Judith

I'm finally getting around to this one. Sorry it took so long.

For two-channel data, no changes should be made to the data when it is
plotted in the trend viewer. However, for single-channel data, there is a
normalization step. The details are listed below. Which data type are you
analyzing? I don't think there is a way to export intensity data without
the normalization (until v4.0 at least).

cheers

Wayne



Here is the scope on the Trend Viewer:

For Ratio Data, nothing is done when it is plotted in a trend viewer. I
have verified that data (sequence level) in the Trend Plot are the same
values as displaying a table (sequence level) for each experiment. To do
this do the following:

-Make a trend plot
-view the trend plot
-select one sequence
-open table view for one of the experiments/profiles that is apart of the
trend plot
-broadcast the selection of the trend plot to the table view
-right-click on the selected sequence in the trend plot and choose
Properties (will show values for all experiments in trend plot for that
sequence)
-compare sequence value in table for experiment to value in the properties
table that appears.
-All is the same!

However!!!
If you are looking at a Trend Plot for Intensity Profiles/Experiments, the
data in the Trend Plot are scaled (by design) and thus will be different if
you try to compare to a table of the same sequences in one of the
profiles/experiments.

How is the data scaled? Glad you asked. Hang on!

Two selection criteria are used:

1) Only positive intensity values are used
2) Of those, the top 10% are stripped (removed) (or only the lower 90% are
used)

Then, for each profile/experiment a mean is calculated (m1). Then, all the
means for each profile/experiment are then averaged (m2). SO now we have an
average of the averages. We next divide the average of the averages (m2) by
the average (m1) for a particular profile/experiment and then multiply this
value with the intensity value for each sequence in that profile! In
formulaic terms:

(m2/m1 (of Profile A)) x (Intensity of Seq. A of Profile A) = scaled
Intensity of Seq. A for Profile A

-----Original Message-----
From: Boer, J.M. (HKG) [mailto:J.M.Boer@lumc.nl]
Sent: Friday, February 14, 2003 3:03 PM
To: Wakeman, Wayne
Subject: export data


Hoi Wayne,

Sorry that I keep asking, but as I go along with using Rosetta, always
something new comes up. You mentioned we could export easily all intensities
and errors for a series of chips in the trend viewer. Indeed I can, but if I
compare back to the original profile intensities and errors and backgrounds,
etc. the numbers are somewhat different! What is happening in the trend set?
I would like to be able to compile the profiles without any changes to the
values!

Judith
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