Report bugs and request features by sending email to: laheyer "at" davidson "dot" edu
1) Segmentation does not have a progress bar or any "I'm busy" icon.
2) On the Mac, the zoom tool is buggy. It only draws zoom boxes from the Y-axis and moves towards the left. To get this function to work, you must click the mouse, hold down the control key, then move the mouse to adjust the box size.
3) Tiff files are very large, and if you load several (number depends on computer), MAGIC Tool may crash. The way to
prevent this is to quit and restart MAGIC Tool after a couple rounds of loading tiff files.
We believe this can be fixed by telling MAGIC Tool to purge each time a new tiff
file is loaded and hope to make this improvement with the next release.
4) Log transformation errors are not specific to the problem. These are usually caused by ratios of 0, since log(0) is not defined. We plan to improve the error message and provide the option to change all 0's to a very small number.
5) Raw intensity values for red and green foreground and background are not saved in segmentation step. We plan to address this limitation soon, beginning with writing a file of raw data, and eventually providing functions for filtering and exploring the file.
6) Error messages in segmentation step not specific to the problem. May be caused by user not have permission to write to selected file location. We are investigating other potential causes of these errors.
7) Spots cannot be flagged for poor quality or low intensity in either channel
This version saves raw data. When you do segmentation, the program will ask if you want to save ratios, but also lets you save raw data. You will get a file with a .raw extension that will show up inside its own folder in your project. The file has 8 columns, with all the values from segmentation: Red foreground and background, both average and total signal. To compare different arrays, you would have to merge the appropriate columns from raw files into an expession file that could be analyzed further in MAGIC Tool or in Excel.
This version has not been extensively tested. Use with caution and please report bugs.
- Infinitely adjustable upper limit on contrast bar in gridding window
- Lifted limitation of gene lists to certain number of total characters (regardless of number of genes). Thanks to Daron Bernard for reporting and testing.
- Lifted limitation on number of genes that can be clustered with hierarchical algorithm
- Increased contrast to 20X in gridding window
- Red/Green color scale in table & tree table corrected (was reversed)
- slider bar to adjust color added to list & tree windows
- groups are made available directly after being created (instead of exiting & coming back)
- in group lists, "control" key now selects individual files
- scramble gene names removed
- canceling a "load saved grid" dialog closes the dialog
- default names for saving and loading fixed
- fixed number of decimal places in view/edit expression data
- new windows in MAGICtool are now brought to front on creation
- regression equation and R^2 now listed
- average replicates fixed
© Copyright 2003 Department of Biology, Davidson College, Davidson, NC
28035
Send comments, questions, and suggestions to: laheyer "at" davidson "dot" edu