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J-Express Pro User’s Manual
Click the Update Selection filter to select all profiles not excluded by the current filter
settings. This selection takes effect in all windows in J-Express Pro, so if you for instance
have a Gene Graph window open simultaneously, the selected profiles can be highlighted
using the shadow unselected feature, etc.
Click the Create Group button to create a new group based on the profiles retained by
the current filter settings.
Click the Create Dataset button to create a new node in the project tree containing the
profiles retained by the current filter settings.
Click the Close button to close the Filter dataset window.
J-Express Pro User’s Manual
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Log(10) Transform All Data – this method transforms the currently selected
dataset into its logarithm (base 10). The data cannot contain any negative
values.
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Log(2) Transform All Data – this method transforms the currently selected
dataset into its logarithm (base 2). The data cannot contain any negative
values.
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Shift All Data To Positive Values – this method shifts the entire dataset a
constant amount along the Y-axis so that no profile contains a negative value.
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Shift All Data To Negative Values – this method shifts the entire dataset a
constant amount along the Y-axis so that no profile contains a positive value.
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Shuffle Columns/Rows – this method shuffles columns or rows, respectively,
based on a random algorithm. Check the Include former Column/Row
Indexes to keep this information in the new node as a reference.
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High Level Mean Normalization – this method performs a high level mean
normalization on the data in placed in the new node.
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High Level Mean and Variance Normalization – this method performs a
high level mean and variance normalization on the data in placed in the new
node.
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Scale Normalization - this method performs a scale normalization on the data
placed in the new node.
3.15 Creating a Sub data set
See
Normalization for cDNA microarray data: a robust composite method
addressing single and multiple slide systematic variation.
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP.
Department of Statistics, Helen Wills Neuroscience Institute, University of
California, Berkeley, CA 94720-3860, USA.
Nucleic Acids Res. 2002 Feb 15;30(4):e15.
J-Express Pro provides a number of methods of modifying a dataset to suit your needs. To
create a sub data set of a currently selected node in the project tree, click the Create Sub
) from the J-Express Pro tool bar, or select Dataset | Create Sub
Data Set button (
Data Set from the J-Express Pro menu bar. The Create Sub Node window will open.
Select the operation you want to perform on the data by clicking the radio button next to it,
and then click Ok. A new node containing the result of the chosen method will be created
below the current node in the project tree.
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Round Decimals - this method creates a dataset with values rounded to the
given number of decimals. Keep in mind that if this number is lower than the
number of number of Maximum Fraction Digits (see Section 3.1.12), the
rounded decimals will be replaced by zeros.
Replace NaN - NaN values in your dataset can be replaced by a fixed number.
Check Fixed Number checkbox and enter a number in the text field provided.
If you want to keep the Missing Value Indices, uncheck the Remove Missing
Value Indices checkbox.
Copy All Data – this method simply copies all the data in the currently
selected node.
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