Sort by Slide Row sand Slide Columns will keep the order of data items (spots) in the mev/tav files as the same in the ScanArray files. If you want to attach all information in ScanArray file that is not used in the tav file, check the Keep All Information in the ScanArray Files. This function is not applicable for converting mev file. The annotation information in txt file will be saved to an annotation file with .ann as file extension automatically.
The mev file always has IA with Cy3, but ScanArray file does not. It could have its channel 1 with Cy5. In this case, the Swap Channel should be checked to ensure mev file to have IA with Cy3.
