The Navigator

Overview

The upper left pane of the GeneLinker™ window is called the Experiments, Genes, or Gene Lists navigator depending on which of the tabs is selected. GeneLinker™ displays the Experiments tab by default. All items listed in the navigator have already been saved to the GeneLinker™ database.

The Experiments tab displays all your datasets and experiments in a hierarchical tree.
The Genes tab displays an alphabetical list of all of the genes in your repository.
The Gene Lists tab shows an alphabetical list of all of your gene lists.

Navigator (Experiments, Genes, Gene Lists)

Icons Used in the Experiments Navigator

Icon	Type of Item
	A complete dataset (raw, preprocessed).
	An incomplete dataset.
	A complete dataset with variable information.
	An incomplete dataset with variable information.
	F-Test results item.
	A hierarchical clustering experiment.
	A partitional clustering experiment.
	A SOM experiment.
	A PCA experiment.
	Discretized data.
	SLAM results.
	Trained ANN classifier.
	IBIS search results.
	Trained IBIS classifier.
	Classification results.
	An annotated item (icon to the right of the name).

An experiment item (clustering, SOM, PCA, etc.) is tagged with an icon appropriate to the process that created it.

Default Dataset or Experiment Names

Imported files, see Import for an explanation of where the dataset name comes from.

For all generated datasets or experiments, GeneLinker™ provides a default name. The default name is based on the type of process (and its parameter settings) used to create it.

Example Dataset/Experiment Names

Removed: v <= 7.6

Removed: p > 0.65

Estimated: #mv < 5 | mean

Estimated: #mv < 8 | nn=2 | euclid

Estimated: #mv < 5 | v=17.078

Filtered: keep {myGeneList}

Filtered: remove {your Favourite Gene List}

Filtered: n-fold with n >= 2.5

Filtered: range #=256

Norm: log2

Norm: Sample scaling: divide, mean=6.7

Norm: Sample scaling: subtract mean

Norm: LinReg: [16-ALL B] | {likelyC56}

Norm: Lowess: window=0.25

Norm: Neg ctrls: {u14-P inhibitors} | median | all samples

Norm: Pos ctrls: {some other gene list} | mean | each sample

Norm: Divided by max

F-test: "my Variable name here"

K-W test: "my Variable name here"

Hier: genes | Euclid | single

K-means, k=4: samples | Chebych | complete

J-P (4, 2): samples | Manhatn | avg

SOM: samples | 5x4 | Spear

PCA: genes

Discretized: 6 bins/sample | quantile

SLAM: "my Rep Variable #2" | 10,000 | 2 | 0.6

ANN: "leukemia-Dr D" | 16-5-3 | N=10 | 0.001 | 15

IBIS search: "Awl or AML test" | LDA | 1D

IBIS: "leukemia-Dr C" | QDA | 2D | N=10

IBIS: "leukemia-Dr A" | UGDA, ALL | 1D | N=10

myNewVariableName

Profile: {avg custom} | Spear