Experiment Performed Using:
* File must be a MS Excel Sheet (in .XLS format, not .XLSX).
Excel Templates for Formatting your Experimental Data:
Cataloged PCR Array
Custom PCR Array
For Custom PCR Arrays - Data Analysis Patches
Convert your custom array raw data into the compatible format for your
customized Data Analysis Template.
Example: Properly Formatted Data Upload Templates
New to RT² Data Analaysis? Learn more by:
- Please note that you must complete all of your work with the PCR Array Data Analysis Web Portal in the same session. Your data is not stored on a server, so all work is lost once the session (or your web browser) is closed. Be sure to export all processed data and results to an Excel file saved on your local computer.
- Please set your screen resolution to 1024 X 768 or greater, if
- Turn off any window pop-up blockers. The software will launch separate
windows for viewing the plots and charts.
Choose the experiment that was performed:
Standard/Cataloged RT² Profiler PCR Array, Custom RT² PCR
Array or individual assays
If you selected Standard RT² PCR Array then Enter the PCR Array Pathway Number from the drop-down list.
If you selected Custom RT² PCR Array then Enter the Custom
Array ID (ex. CAPX####) in the text field.
- If your experiment used individual primer assays then select Single or Multi-Gene qPCR Assays.
Browse and select the MS Excel file
containing your PCR data with a maximum number of 100
samples. Click "Upload".
Analysis Setup page:
In the "Basic Setup" section, assign samples
to different groups. At least two groups are needed,
where one of those groups must be the control group.
Click "Update" when finished. You may exclude
samples from the analysis by selecting
"Exclude" on the drop down menu.
Review the "Data QC" section to assess each
groups' PCR reproducibility, reverse transcription
efficiency, and the presence of genomic DNA
The "Select Housekeeping Genes" section allows
you to remove or add preferred housekeeping genes for data
normalization by clicking the appropriate checkboxes. Click
"Update" when finished.
Review the "Data Overview" section to see each
group's distribution of threshold cycle values and the
average of the raw data in each group.
- Analysis page:
See the "Average Ct", "2^(- Ct)", "Fold
Change", "p-value", and "Fold
Regulation" sections for the results processed by the
software from your data. The "Fold Change" and
"p-value" results are used by the software in
subsequent graphical analyses.
- Plots and Charts
Define Groups to be compared and whether to report the
fold-change results as a log transformation or not
(default recommended). Click "Update" once
changes have been made. Click "Export Data"
to download the results as an Excel file.
Scatter Plot and Volcano Plot
Define Groups to be compared. Choose the fold-change
boundary (and p-value for Volcano Plot) of interest.
Click on symbols to identify gene and fold-change (and
p-value for Volcano Plot); mouse over table entries to
point to symbol on plot.
Click check boxes to remove genes from or add genes to
plot. Click "Update".
Click "Export Data" to download the results as
an Excel file.
- Sort samples by "Array" or by "Group".
- Select "Join Type". The default of "Average" is
- Cluster in "1-D" by genes only or in "2-D" by genes
- Color code the graph by "Genes", "Samples" or
"Entire Dataset". The default of "Genes" is recommended.
- Choose whether or not to display the gene symbols and array or group
- Click check boxes to remove genes from or add genes to plot.
- Click "Update".
- Multigroup Plot
Click check boxes to add genes to or remove genes from plots.
Choose results to plot on the y-axis, either "AVG Delta Ct",
"2^Delta Ct", or "Fold Change".
Review either the line plot (above) or the column chart (below).
- Click "Export
Data" to download a MS Excel file containing all raw
and processed data from the "Readout" and
"Analysis Result" sections.
Examine experimental solutions for
identifying the mechanisms behind the
observed changes in gene expression.