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Dictyostelium discoideum
Array Tools

Introduction dummy
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:
  • Import ScanArray Express CSV to Excel.
  • Export the data to R by creating Data.spot, R Commands. R and Arrays.txt files.
  • Re-importing data from R to Excel.
  • Exporting data to SAM

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Figure 1: Array Tools 3.3 (2004), Download (Excel file, 722 KB)

Usage
1. Experiment dummy
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 dummy
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.
  1. If one microarray data file is selected the data will be imported.
  2. If two data files of the same microarrays scanned with different laser powers are selected, the saturated spots of the high laser power scan will be replaced by non-saturated spots from the low laser power scan.
The Option "Spotting Solution" allows the text string identifying the spotting solution to be modified. This may be necessary if the spotting solution is changed, as the import also performs data filtering by flagging spots as "Bad". Data filters are:
  1. Spot intensities below or equal to zero.
  2. SpotReport spots, identified by the string "SpotReport".
  3. PCR negative controls, identified by the string "PCRNeg".
  4. Empty spots, identified by the string "<>" or "emp".
  5. Spotting solution.

3. Export to R dummy
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 dummy
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 dummy
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.
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September 12, 2013
Institute of Biochemistry I, Cologne
Suggestions and wishes: Gudrun Konertz
Voice: +49 221 4786930
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