How can I export my spot data?
Melanie allows you to export a table with all spot data, also called project data. You can use the exported file for further analysis of your experiment with third party software. To export your project data, click the Project icon at the top left of the screen and then choose Export > Data > Save to file.
NOTES
Data export is only available in certain workflow steps.
- For expression analysis: in the Review and Results steps.
- For coverage analysis: in the Spot edition and Coverage steps.
Data exports are context specific. Most of the exported fields will be the same between different data exports. But other fields will be available only in a particular workflow step. That is, the list of exportable fields will be different between the Review and Results steps. There will also be variations between different types of analyses (e.g. One-factor analysis or Two-factor analysis in the Classic and DIGE modules) or between exports for different image pairs (for the Coverage module).
TIP
Depending on the export format, the exported data and the export options, the generation of your file can take a significant amount of time. This is particularly true if the table contains images to be exported (such as Bars, Histograms, 2D views, 3D views, etc.). We therefore recommend you initiate the export when you can walk away from your computer to do something else. A coffee or lunch break are ideal moments!
Export formats
The following export formats are supported:
- Tab-delimited Text format (.txt)
- Excel Workbook file (.xlsx)
- HTML (Web document) (.html)
- XML format (.xml)
Exportable data
Expression analysis
The following data can be exported for Single stain, DIGE with internal standard and Multiple stain without internal standard projects.
For data export in the Review and Results steps
- ID: Spot ID
- Pixel X, Pixel Y: Coordinates of the spot on the global reference image (cropped).
- pI, MW: Calculated pI and MW of the spot (only available if pI and MW markers have been defined).
- Area [Image name]: Surface delimited by the spot border, expressed in mm2. The same spot can have slightly different areas on the different images due to the spot being warped proportionally to the deformation calculated in the alignment (when spots are propagated from the fusion image to each individual image).
- Intensity [Image name]: The intensity of a spot is based on the highest gray values in the spot from which the background has been withdrawn. The background is defined as the minimum gray value on the spot border. This intensity is calculated on raw pixel values, before normalization was applied.
- Normalized intensity [Image name]: This is the intensity (as defined above) calculated after application of normalization.
- Volume [Image name]: The volume of a spot is the sum of the background-subtracted gray values of all pixels delimited by the spot border. The background is defined as the minimum gray value on the spot border. This volume is calculated on raw pixel values, before normalization was applied.
- Normalized volume [Image name]: This is the volume (as defined above) calculated after application of normalization.
- Vol Ratio [Image name]: The volume ratio is specific for DIGE experiments with internal standard. It is the volume of the spot in the current image divided by the volume of the spot in the DIGE internal standard image.
- Bars: Graphical representation of the expression profile, without scale, mean value(s) and dispersion interval(s).
- [Spot set name]: The value Yes in the export indicates that the spot belongs to the spot set, No indicates that it does not belong to the spot set.
- [Annotation category name]: The value in the export is the label for the spot in the particular annotation category.
Only for data export in the Review step
- Mean: Arithmetic mean of the spot value across all images.
- SD: Standard deviation of the spot value across all images.
- CV: Coefficient of variation (SD divided by the Mean) of the spot value across all images.
- Range ratio: Maximum spot value divided by the smallest spot value for the spot across all images.
- Excluded: Indicates whether the spot was excluded from the analysis (1) or not (0).
- Edited: Indicates whether the spot was edited (1) or not (0).
- [Image name]: Choose a spot value in the Group table of the Review step to export this spot value for each image.
- [Image name] Image: Export the 2D view of the spot for the image.
Only for data export in the Results step
- Histogram: Expression profile with vertical scale, mean values and dispersion intervals.
- [Treatment name]: Mean spot value for the treatment group. The spot value used is indicated in the Parameters section at the top of the file).
- Max: Highest mean spot value across all treatment groups.
- Fold: Highest mean spot value across all treatment groups divided by the lowest mean spot value across all treatment groups.
- Anova (p): Anova probability (for One-factor analysis).
- Factor 1 (p), Factor 2 (p), Interaction (p): Anova probabilities (for Two-factor analysis).
- Analysis-X: Spot validation status (Included, Excluded or Not reviewed) for the analysis with identifier X.
- Validation: Spot validation status (Included, Excluded or Not reviewed) for the entire experiment.
Coverage analysis
The following data can be exported for Coverage and Coverage DIGE/DIBE projects.
For data export in the Spot edition and Coverage steps
- ID: Spot ID
- Pixel X, Pixel Y: Coordinates of the spot on the global reference image (cropped).
- pI, MW: Calculated pI and MW of the spot (only available if pI and MW markers have been defined).
- Area [Image name]: Surface delimited by the spot border, expressed in mm2. The same spot can have slightly different areas on the different images due to the spot being warped proportionally to the deformation calculated in the alignment (when spots are propagated from the fusion image to each individual image).
- Intensity [Image name]: The intensity of a spot is based on the highest gray values in the spot from which the background has been withdrawn. The background is defined as the minimum gray value on the spot border.
- Volume [Image name]: The volume of a spot is the sum of the background-subtracted gray values of all pixels delimited by the spot border. The background is defined as the minimum gray value on the spot border.
- Bars: Graphical representation of the expression profile, without scale, mean value(s) and dispersion interval(s).
- [Spot set name]: The value Yes in the export indicates that the spot belongs to the spot set, No indicates that it does not belong to the spot set.
- [Annotation category name]: The value in the export is the label for the spot in the particular annotation category.
- [Image name] Image: Export the 2D view of the spot for the image.
- [Image name] 3D Image: Export the 3D view of the spot for the image.
Only for data export in the Spot edition step
- Mean: Arithmetic mean of the spot value across all images.
- SD: Standard deviation of the spot value across all images.
- CV: Coefficient of variation (SD divided by the Mean) of the spot value across all images.
- Range ratio: Maximum spot value divided by the smallest spot value for the spot across all images.
- Excluded: Indicates whether the spot was excluded from the analysis (1) or not (0).
- Edited: Indicates whether the spot was edited (1) or not (0).
- [Image name]: Choose the spot value in the Group table of the Spot edition step to export this spot value for each image.
Only for data export in the Coverage step
- Status: Coverage status for the spot, for the specific coverage pair (2 images).
- P:State, S:State: Spot state (Absent, Present, Uncertain) on the primary (P) and secondary (S) image, respectively.
- P:Intensity, S:Intensity: Intensity of the spot in the primary (P) and secondary (S) image, respectively. The intensity of a spot is based on the highest gray values in the spot from which the background has been withdrawn. The background is defined as the minimum gray value on the spot border.
- P:Vol, S:Vol: Volume of the spot in the primary (P) and secondary (S) image, respectively. The volume of a spot is the sum of the background-subtracted gray values of all pixels delimited by the spot border. The background is defined as the minimum gray value on the spot border.
Export options
The export options allow you to tweak the output:
- Rows – Specify if you want to export all rows (spots) or only selected rows (spots).
- Columns – Choose if you want to export all columns, visible columns or a specified subset of columns.
- Description – Indicate if the output should contain information about the report.
- Extended headers – Tick this option if you want to include information about the factor level(s) to which each image belongs.
- Cell colors – Tick this box if the colors of the cells as they appear in the table should be exported as well.