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Array Tools is an Add-In for Microsoft Excel, which is designed to handle the import and export of Dictyostelium discoideum microarray data. It can be used to:
Figure 1: Array Tools 3.3 (2004), Download (Excel file, 722 KB)
This tab is used to open, close or create a new Experiment file. An Experiment file is an Excel workbook, that serves a container for all the microarray data of an experiment. it can contain the imported, R and SAM worksheets for as many microarrays an experiment is composed of.
2. Import from ScanArray Express
This tab is used to open ScanArray Express CSV files in Excel. Note that the suffix of the CSV files has to be changed to *.txt. Several files may be selected and opened in one go. Opened files can subsequently be imported to the Experiment file in two different ways.
3. Export to R
This tab is used to create the files needed for data normalization using R. "Export to R" writes a *.spot file for each microarray of the experiment, which contains the M- (ratio) and A- (intensity) values. "Create R Commands file" writes a script of R commands, that instructs R to normalize the data. As this commands script contains the paths to the *.spot, GAL and Arrays file, all these files have to be saved in the same folder. The GAL needed for R is one without a header. Array Tools prompts the user for the GAL file to determine the path of all the files for R. "Create R Arrays file" writes a text file containing the barcodes of the experiment's microarrays. The option allows the user to choose, whether background should be subtracted.
4. Import from R
This tab is used to import the normalized output from R, by selecting a microarray from the list and choosing the according Rout file.
5. Export to SAM
This tab is used to write the normalized M values into a new worksheet for SAM analysis. In this step all probes spotted in higher replicates are reduced to double spots by averaging. Furthermore all probes that are flagged "Found" in less than half of the spots, are excluded from SAM analysis.
September 12, 2013
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