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As previously described (Thimm et al. [2004]), an Oryza sativa map was developed and uploaded to MapMan, and the change in expression ratio of each gene was calculated as the log2-fold change to generate the MapMan experimental file.
Three figures, five tables, and one experimental file.
All spectra were collected together into one experimental file.
The change in expression ratio of each gene was calculated as the log2-fold change to generate the MapMan experimental file.
The microarray suite references the experimental file to select an analysis algorithm for a cell intensity file that generates a gene chip file.
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All data collected from individual arrays used at the same settings were saved in a separate experimental files e.g. WCX low laser S1, SAX high laser S2.
The Graphical User Interface (GUI), written in English, allows for quick selection of experimental files and setup data files; it includes functions for folder processing and basic image manipulation.
Experimental Model file (an AnimateLab project file).
Further, our implementation has been automated for Affymetrix short oligonucleotide microarrays and can generate a list of candidate SFPs when provided only with an experimental design file pointing to raw.CEL files.
Raw and normalized data files and experimental design files are available at the NCBI Gene Expression Omnibus (GSE38084).
For example, one of the most frequently used data processing tools in computational proteomics, Max Quant uses an experimental design file to assign raw data files to the experiment to which they belong [ 21].
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