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INFINICYT®VERSION 1.2
To improve the benefits that this software
offers, Infinicyt®1.2 has increased the speed ofdata processing and has included
the following functions:
1. MANUAL ANALYSIS1.1. Reference
Image……..……………………………….………………………….……..
2. Virtual
Parameter.…...………………………………………………..……..…..…..…
3. Diagrams1.3.1. The new option in the
toolbar: Diagrams …………………………………….
21.3.2. New type of diagram to represent
the results: Box Plot …………………..…...
31.3.3. Options to smooth the contour and
auto-regulate the maximum value to shownin the histograms…………………
41.3.4. Representing density plots with
contour lines……………………….…..……..
41.3.5. Show the scale of axes in
the Parameter Band Dot Plot…………..……………
51.4. Statistics window of the Profile
Configuration.………………..….………….….…….
61.5. Comments: 1.5.1. Possibility to see
the comments associated with a file ($COM)……………....
61.5.2. Column of “Comments” in the
analyzerYou can configure number and name of the column “Comments”…….…
7Icon notice in the analyzer if there are
comments …………..……..……….
71.6. Save analyzed files 1.6.1. Save
files in anonymous format………………………..…………………….…
81.6.2. Option to show or not a message of
changes in current analysis…………..….
82. FILE MERGE: 2.1. Merge a FCS file with
an already analyzed file (.cyt format).........................................
92.2. Controls icons in the analyzer……………………………………………………….....
92.3. Options to select how to identify
the different tubes merged in the analyzer……….…
103. FILE EXPORT3.1. Export the results of
the report to XML format ……………………….……………….
113.2. Export several linear parameters
with the SSC-low transformation applied…………...
114. GENERAL OPTIONSSaving an FCS file
with FCS or TXT format……………..……...……………………..
MANUAL ANALYSIS- 1 -1. Reference Images. In the version 1.2 of Infinicyt®, it is
possible to save pictures of the diagrams which can be used as areference in
similar data files to analyze. This reference pictures can appear as background
picturein the same dot plot you are analyzing so you can always have the
reference image to compare withthe current file. See detailed information about
reference images in chapter 5.1.5.6-8 of the User’sManual and several
illustrative examples in the tutorial “Reference Image” available in our
website: www.infinicyt.com. To create a reference image the user has to consider
that the data file of reference and the data fileto compare later, need to have
exactly the same parameters acquired. Once this is checked, the useranalyses the
data file of reference showing in the population tree only the populations of
interest,clicks the option “Save Reference Image” from the Profile menu, and
gives a name identity. Thisprocess allows us to save the graphic and statistical
data of the selected populations from theoriginal file. Reference images are
part of the profile so to use the reference image saved in other files, we
mustupdate the current profile (click “Save profile” from the Profile menu), or
save the analyzed filewhich contains the reference image (click “Save Analyzed
file” of the File menu) because this willautomatically save the profile used for
the analysis of the data file of reference. To use in other files the images of
reference and its statistical data previously saved, simply selectthe option "Load
reference image" of the Profile menu and select the name assigned. The reference
events will appear in a new label ofthe population tree and we can hide or show
themclicking on the VIS box. By right-clicking on thenew label, the user can
edit the appearance ofthese reference events changing the color,displaying them
as dots, contour lines, densityisolines, etc.
MANUAL ANALYSIS- 2 -2. Creating Virtual Parameters In the version 1.2 of
Infinicyt®, it is possible to create new analysis parameters calculated
asmathematical functions of parameters present in the data file. See detailed
information about virtualparameters in chapter 5.1.5.9 of the User’s Manual and
several illustrative examples in the tutorial“Virtual Parameters” available in
our web site: www.infinicyt.com.To create a virtual parameter, select the option
“Virtual Parameter” of the Profile Configurationmenu and click on “Add” button.
Then, you must give a name identity and define the mathematical formula that the
program willapply. The way to define the virtual parameter formula is similar to
create new statistics. Each new virtual parameter can be displayed in different
types of graphics so that the graphicrepresentation of each event is the result
of the mathematic formula already defined. 3. Diagrams3.1 It has been created a
new menu in the toolbar called “Diagrams” which includes differentoptions
relating to graphic representations. In earlier versions of the program these
functionswere located in other menu options. It has been introduced as new
control commands: Ctrl. + T for selecting the option “Tile”which resizes
diagrams to cover the whole screen of the computer.
MANUAL ANALYSIS- 3 -3.2 New type of
diagram to represent the results: BoxPlot. This type of graphic can be useful to
display differences between populations without makingany assumptions of the
underlying statistical distribution. The spacings between the differentparts of
the box help indicate the degree of dispersion (spread) and skewness in the
data, andidentify outliers. Boxplots are especially useful when comparing two or
more sets of data. When you choose a BoxPlot as new graphic, the diagram will
represent in the X axes all thepopulations visible in that moment in the
population tree, and in the Y axes you can choose theparameter to represent. -
The box itself contains the middle 50% of the data. The upper edge (hinge) of
the boxindicates the 75th percentile of the data set (third quartile x.75), and
the lower hingeindicates the 25th percentile (first quartile x.25). - The line
in the box indicates the median value of the data (x.50). Thus, if the variable
issymmetrical, that line will be located in the centre of the box. - The ends of
the vertical lines or "whiskers" indicate the values that differ by more than
1.5times the distance interquartile and are calculated by multiplying the
distance interquartile(x.75 - X25) x 1.5. - The points outside the ends of the
whiskers are outliers and they can show in the diagramactivating the option
“Show extreme values” in the BoxPlot Configuration window. See detailed
information about BoxPlot diagrams in chapter 5.3.5 of the User’s Manual.
MANUAL ANALYSIS- 4 -3.3 We have included
new functions relating to Histograms to improve the visualization of thepeaks.
Selecting the option “Histogram Configuration” from the Diagram Configuration
menu,you reach a new window that allows to smooth the contour and auto-regulate
the maximumvalue to be shown in the histograms. When the extreme values of the
histograms are very highdo not let to clearly visualize the lower values of the
other peaks, in such cases auto-regulationcan hide the extreme peaks of the X
parameter to better visualize the central peaks of thehistogram. 3.4 It has been
added the ability to view density plots with contour lines. In version 1.2 of
theprogram, the user can visualize density plots as points, contour or both. -
To apply this option to a specific diagram, you must right-click on the diagram
and selectthe desired option from the “Density Configuration” window. - To apply
this option to all the diagrams with the density option activated (Total Density
orPopulation), you must select the type of density representation from the
ProfileConfiguration window.
MANUAL ANALYSIS- 5 -3.5 The new version of Infinicyt®shows the scale of each
band in the Parameter Band Dot Plot
MANUAL ANALYSIS- 6 -4. Statistics window of the Profile ConfigurationIt has
changed the visualization of the available functions in the Statistic window of
the ProfileConfiguration:The option to calculate absolute counts from the
reference population selected by the user isnow available at the top of the
window.In reference to statistics functions to visualize in the population tree:
o It has changed the way user selects the statistical functions to visualize in
thepopulation tree. o This new version allows us to create as many new functions
(mathematical formulas)as needed.5. Comments5.1 We can access comments
information saved during the acquisition of the file ($COM),from the option
“Info” of the File/Properties menu. When we are analyzing a merged file, wewill
see also the name of the original files.
MANUAL ANALYSIS- 7 -5.2 Column “Comments” in the analyzer5.2.1 As a default the
analyzer will show only one column for comments about the differentparameters of
the sample, but we can configure number and name of the column“Comments” from
the Profile Configuration window. 5.2.2 If there are comments about the
expression of a parameter in a population, in the analyzerwill appear an icon of
notice.
MANUAL ANALYSIS- 8 -6. Save analyzed files6.1 From the window "Save As…" of the
Save Analyzed File / File menu you can choose theparameters to save of the
analyzed file and anonymize its information. This function isalso available from
the options File Export and File Edit of the main menu window. 6.2 From the
Analysis/Profile Configuration window you can deactivate the option to show
awarning reminding to save the analyzed files when you finish. If you deactivate
this option,the files analyzed won’t be saved unless you do it through the
option Save Analyzed File of theFile menu.
FILE MERGE- 9 -1. Merge a FCS file with an already analyzed file (.cyt format)In
the 1.2 version of Infinicyt®, you can merge a FCS file with an already analyzed
file .cyt. Inthis case of merging files, you will have to choose “all Files” in
the option “Files of type” inthe “Select Files” window, so you will have both .cyt
and .fcs files available to merge. 2. Controls icons in the analyzerIt has added
in the analysis window new control icons which will appear on red color if
thesoftware finds important differences related to the coherence controls among
the files(M=Merged Control, P= Population Control).
FILE MERGE- 10 -3. Options to select how
to identify the different tubes merged in theanalyzerIn earlier versions of the
software, the different tubes merged in a file were named in analyzerand report
only by file number. Version 1.2 lets you choose from Analysis/ProfileConfiguration
window, how to identify the merged files: by number, name or comment.
FILE EXPORT- 11 -1. Export the results of the report to XML formatThe Extensible
Markup Languaje (XML) is used for exchanging structured information
betweendifferent platforms. It can be used in databases, text editors,
spreadsheets, etc.The version 1.2 of Infinicyt® gives the option to save the
results of the report in this format. Youwill find this option in “Files of
type” of the “Save As…” window of the Report. 2. Export several linear
parameters with the SSC-low transformationappliedIt has added the possibility to
export the mathematical transformation to improve the separationbetween
populations in the lower part of the scale to several parameters with linear
scale. In otherversions this option only was be able to be applied to the SSC
parameter. This option is availablein the checkboxes of the Advanced/File Export
window.
GENERAL OPTIONS- 12 -Saving a FCS file with FCS or TXT formatIn the version 1.2
of Infinicyt® it is possible to save the results of a FCS file in TXT format.
Youonly have to choose this option in “Files of Type” of the “Save As …” window.
This window isavailable from “File Export” and “File Editor” of the main menu
window, and from “SaveAnalyzed File / File” menu of the analyzer.
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