User support and trouble-shooting guide

Please send dChip usage questions and discussions of microarray data analysis to dChip Yahoo group, and send function suggestions and bug reports of dChip to Cheng Li (cli@hsph.harvard.edu). It will be helpful if the followings are attached with email for diagnostic purpose: dChip version and downloading dates, analysis outputs and error messages (use “Analysis/Copy” or “Analysis/ Save”), dChip exported data and image files, parameter files (with .INI extension and in the same directory as dchip.exe), or the screenshot (Press PrintScreen key and paste into Paint software to save). If dChip crashes or you observe strange things happening, you may also try one or more of the following:

· In the clustering picture, the part of figure is overlapped or not displayed: use Arrow keys, Control+Arrow keys and Shift+Arrow keys to adjust.

· Click the "Tools/Options/Reset Default" button to reset settings, or delete the existing “group_name”.ini files (in the same directory as dchip.exe) and then restart dChip.

· Download and use the latest version of Gene information files or dChip itself. If needed copy these files and the CEL data files (but not the *.ini files containing dChip settings) into a new directory, and start dChip from here.

· Change to another PC or Windows system.

· When opening a group, check “Open group/ignore existing DCP file” and “Open group/Other information/ignore existing cdf.bin file” to re-extract the CEL and CDF files.

· “Gene information file” may have been saved in Excel format. Open files in Excel and use “File/Save As” to save in tab-delimited text format.

· If “out of memory” when clustering many genes, you can uncheck “Tools/Options/Clustering/Pre-calculate distance” before clustering.

· Clustering image exporting problem.