GV Exercise.3
Export from Genevestigator
[ Main_Page | Genevestigator_training | Analyze_public_microarray_data_using_Genevestigator | GV Exercise.2 |
| GV Exercise.4 ]
last edit: November 09, 2014
Contents
Aim
- Use the Sample selections and Gene selections created in the former exercises to see the effect and purposes of the different tools.
- Export data and pictures from Genevestigator
- Review more detailed information available from the GUI.
Changing focus
- Load the Exercise-2 workspace in GV (get if here)
- Re-create the metacaspase Gene Selection as seen before and using the TAIR IDs provided below
AT1G02170 AT5G64240 AT1G79310 AT1G79320 AT1G79330 AT5G04200 AT4G25110 AT1G79340 AT1G16420
- Select the metacaspase as Gene selection at the bottom-left of the window.
- Select the Condition Search Anatomy tool from the home page.
- Set the sample selection to methyl viologen : what happens??
try it first
- Select instead the oxidative sample group (253 samples)
- Focus on the first metacaspase (ATMC1) and look for its tissue distribution, then uncheck the first gene and get the result of the second gene, ... etc
Display types
- Alternate between the different display modes to see the data from different angles
- Now change the display to show all metacaspases as heatmap
- How many probes can you view together in Boxplot, Scatterplot, and Heatmap modes?
- What is the additional effect with the -tree modes?
Exporting data
Both data and pictures can be saved from most GV windows through the Results menu Items using bold text menu items
Exporting the normalized expression values shown in a heatmap (color) OR the confidence about these expression levels can prove very interesting in order to replay GV data elsewhere. If you want both values, you will need to export twice (the double-export feature has been requested ;-) )
Export Expression values
- Now set focus on Ath.all and metacaspase_references and use the Condition search Anatomy tool.
Select Export Data... and see what options can be chosen to save the data to your local disk
expression levels and std. deviations' cannot be saved together (the feature was requested to the GV team). If you want both, you will need to export twice and merge the tables in your favourite spreadsheet
Export Pictures
Similarly, images can be saved in different formats with Export Image
PDF is a vector scalable format that will keep better resolution while remaining reasonably small in size
Heatmaps easily span multiple pages in height. In order to keep a good image resolution, please adapt the image size in the Scale image dialog
Sample details
At any time, you can get detailed information about the origin of a given spot. To do so, hoover on the spot with the mouse and freeze the window with the F2 key.
- mouse over the top left spot in the current heatmap
References:
[ Main_Page | Genevestigator_training | Analyze_public_microarray_data_using_Genevestigator | GV Exercise.2 |
| GV Exercise.4 ]
