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All annotations are preserved if the dataset is saved in the data file (*.df) 'native' for ProSeq3.
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Each dataset was saved as an Excel file.
Statistics of our annotation dataset were saved into a Microsoft Excel datasheet, and charts were generated.
Following data normalization, samples were ordered according to tissue type and the dataset was saved as an '.expression' file and then loaded into the network analysis tool BioLayout Express3D [ 30], as described previously [ 31].
Each dataset was saved as an '.expression' file containing a unique identifier for each row of data (Gene symbol concatenated to probeset ID), followed by columns of gene annotations used as class-sets for the overlay and analysis of information with respect to the graph, and finally natural scale normalised data values for each sample (each column of data being derived from a different sample).
Time is saved, too.
Once loaded, datasets may be saved as "sig" format for later analysis or manual editing.
Work on different datasets can be saved into separate sessions, and the sessions can also be combined later if needed.
This resulted in 1000 pairs of training and testing datasets (2/3 and 1/3 of the original dataset, respectively) which were saved for further processing by the neural networking.
Then the predictions can be made and dataset data can be saved for further use by the software.
Statistics that describe datasets X and Y are saved in the summaryX-YACCA.txt and summaryY-YACCA.txt files respectively.
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