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Therefore transformed files were manually reviewed.
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The first step of our method transforms files into a more abstract representation, their logical structure.
The AGCC software (Affymetrix GeneChip Command Console) transformed DAT files into CEL files to change image signals into digital signals, which recorded the fluorescence density of probes.
In fact, the .csv files can be easily transformed into.nirs files.
Then we transformed these files to the input format defined by each NER tool.
Raw signals were transformed into.CEL files in GCOS software (Affymetrix, Santa Clara, CA).
Because the probability of plating independently transformed cell files so closely together was low when considering plating density of ~30 – 50 calli per 6 cm-diameter plate, these cells are likely to represent the offspring of independently transformed cells that were located in a single cell file.
Finally, all sound files were transformed into wave files for stimulation in the scanner (using WaveLab, Steinberg).
These TIFF files are transformed into text files that contain fluorescence intensities for each gene.
In brief, raw sra files were transformed into fastq files using SRA Toolkit available at NCBI.
MGF files were transformed to DTA files using custom Perl scripts and SEQUEST searches performed on the same sequence database through the TransProteomicsPipeline (TPP) software (Pedrioli, 2010).
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