Download GEArray Expression Analysis Suite Tutorial

GEArray® Expression Analysis Suite
Tutorial
Image, Data, and Statistical Analysis
Software Package for the GEArray
from SuperArray
Features & Benefits of
GEArray Expression Analysis Suite
Web-Based Application
Image Analysis
Data Acquisition
Data Analysis
Statistical Analysis
Reports Exported
Log In to Server:
2. Enter Email Address.
3. Enter Password.
4. Click Login button.
http://geasuite.superarray.com/
1. Be sure that latest version of
support software installed and
platform requirements meet.
Create a New Project
Project = One experiment using multiple arrays with the same catalog number
1. Give the project a Name.
2. Choose the Catalog Number
of the array used in the
experiment from the pull down
menu.
3. Provide a brief
Description of the project.
(Optional)
Press Clear to correct mistakes.
Press Continue to create project.
Projects List
Upon pressing Continue, Project will be added to the List.
Click the Project Name to upload Array images into or to edit the Project.
Upload Array Images Into the Project
Specific Project page opens upon initial creation
or by clicking its name from Projects List.
1. Give each array a Name.
2. Browse your file folders for
the File Name of image file.
(Supports many formats.)
3. Provide a brief
Description of each array.
Press Clear to correct mistakes.
Press Continue to upload array image.
Project Page & Array List
Project Information
Edit information if needed.
Arrays List: Contains list
of uploaded arrays and
available information
Clicking the Array Name opens IDEA.
Clicking icon opens Array page to edit info or print hardcopy.
IDEA = Image Data Extraction Applet
Two Workspaces:
Image / Settings
Adjust cropping frame
Optimize array image
Grid / Readout
Align circles to spots
Acquire and save data
Adjust Image Settings
4. Switch to Grid/Readout Workspace when done.
1. Adjust
Crop Frame
to match
Array Image.
Click & Drag
to move & resize.
3. Adjust Upper
2.
& Lower
Brightness
&
Saturation
Contrast
Thresholds.
Balance.
top and
Use left
bottom
sliders.
right
hand
sliders
Sliders adjust appearance of image.
Flip icons
Click Undo
icon to rotate frame
vertically
and/or
horizontally.
to
remove
previous
adjustment.
Toggle
Rotate
Icon
to click & drag Sliders do not affect the data.
Click
Reset
icon
to start all with
over again.
Magenta
spot
Click
icon
Crop Redo
Frame
toshould
matchalign
Array Image.
array
position
1. adjustment.
to
repeat
previous
Data Acquisition
Switch
to Image/Settings
5. Preliminarily
examine
the results byWorkspace
changing: if needed
1. Auto-Align Grid
4. Build Readout
Background
Correction (BC)
2.Density
Auto-Align
(D) Spots
Clover Mode
(CM)
6. Save Readout
3.Density
Adjust menu
size
alsoposition
contains
and
of
gene
list
and
individual spots if
7. Close IDEA
absent / present
necessary
by
when finished.
calls.
selecting
Spots
defined
or(Options
Spot Groups.
on Data
AnalysisGrayscale of cells reflects signal intensity.
(Click
& Drag)
slide.)
Red numbers correspond to “bleeding” spots.
Blue numbers correspond to known negative controls.
Complete Acquisition & Begin Data Analysis
Closing IDEA returns to Project Page where Array now has Readout.
Repeat IDEA for each array in Project.
Once Readout available for all Arrays, click the Analysis link on the top of the page
Data Analysis Window
Arrays
listed horizontally.
Dataset Table: Data
annotated
to genes list vertically.
Array Name links
back to IDEA.
Gene Names link to
NCBI Information.
Dataset Parameters: Correct and Normalize Data (next slide)
Use links in Projects List to load different
Projects into Analysis window.
Defining Dataset Parameters
Clover
Click
Update
Mode:toQapply
Series
anyand
new
low
Dataset
densityParameters
Oligo GEArrays
to Dataset
ONLY Table.
Density:
Off:
from inside
group
Total:Only intensity
Total intensity
insidespot
each
spotcircles reported
On:
Intensity
from
inside andtoinsquare
between
spot groups reported
Average:
Total
normalized
area
Normalization:
Background Subtraction:
No normalization:
correction:
Data is not normalized.
corrected for background.
Selected
Global: Genes: Intensity
Average of
intensity
checked
outside
housekeeping
circles across
gene(s)
entire
spot(s)
area
Median:
Empty Spots:
Statistical
Average intensity
median of
of spots
all intensity
withoutvalues
DNA (blanks)
on array
Interquartile:
Local:
Statistical
Average intensity
median outside
of middle
individual
50 % of circles
intensity values
Minimum Value: Smallest intensity value on the array
Defining Groups
Place Arrays into Groups (up to 9) using pull-down menus.
IMPORTANT: Click Update button to save those definitions.
Group = Set of arrays from experiments conditions with common features
Example include:
Replicate determinations
Tissues from multiple animals with the same genotype or even phenotypes
Biopsies from normal or disease patients
Scatter Plot will average results from all Arrays in one Group and calculate
fold changes in gene expression between Groups.
Exported Expression Results
Click the Export Data link on the top of the Analysis page.
Saves all of the following information into one Excel file:
Raw Data
Analysis Report
Absent and Present Calls
Bleeding
Performance Outline
Scatter Plot
Click the Scatter Plot link on the top of the Analysis page.
User-Defined Settings
Log
transformation
of data from
two different
groups plotted
against each
other
Export Functions
Zoom window
Individual
gene
information
Scatter Plot: User-Defined Settings
Designate Groups compared in Scatter Plot using pull-down menus.
Fold changes in gene expression
expressed relative to X Axis Group.
Designate fold changes in gene expression using the Boundary function.
Scatter Plot: Log Transformation Plot
Red symbols indicate
increase in gene
expression from
X Axis to Y Axis
greater than userdefined Boundary.
Parallel lines
move according
to user-defined
Boundary.
Green symbols
indicate decrease in
gene expression from
X Axis to Y Axis
greater than userdefined Boundary.
Center line (the line
of unity) indicates no
changes in gene
expression.
Each symbol represents one gene.
Black symbols indicate gene expression changes less than user-defined boundary.
Scatter Plot: Gene Info and Export Functions
Save Image for publication quality figure.
Save Dataset to export list of
genes up- and downregulated to Excel file.
Click symbols on full sized image or
zoom window for complete gene
information including fold-change
and link to NCBI entry.
ClusterGram
Click the Clustergram link on the top of the Analysis page.
Organizes genes with similar expression levels across arrays in the same project.
K Means
Click the K Means link on the top of the Analysis page.
Organizes genes with similar
expression levels across arrays in the
same project.
Number of clusters is user-defined.
Export link on top of K means page
reports gene list for each cluster as
an Excel file.
GEArray® Expression Analysis Suite
Tutorial
Image, Data, and Statistical Analysis
Software Package for the GEArray
from SuperArray