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The GCOS v1.2.1 update should only be applied to GCOS v1.2 client and v1.2 Server systems. Other versions of GCOS do not require this update.
GCOS v1.2.1 update is being released to correct a defect in GCOS v1.2 comparison analysis when using Probe Masking (MSK files).
In GCOS v1.2, the CHP file does not store the background values or the probe masking at the end of the statistical analysis. When such a CHP file is selected as a baseline chip file in comparison analysis, the background values of the chip file have to be recomputed. The MSK file is ignored when computing the background values of the baseline chip file. Since the background values are used in comparison calls, a discrepancy will be observed in the comparison calls between GCOS v1.0/1.1 and GCOS v1.2 when a mask file is used. The discrepancy will be observed in all comparison outputs (call, p-value, signal log ratio, SLR High and SLR Low). Since the comparison results differ, so will the Expression Report.
The GCOS v1.2 CHP files are exported in a manner such that the background values are re-calculated and written out as a float. If the CHP file was created using a MSK file, the exported CHP file will not have the same background information as the masking information that would normally be stored in the MAS 5.x CHP file.
GCOS v1.2 displays the background-subtracted intensities as a bar graph in the Expression Analysis Window (EAW). If a MSK file was used for CHP analysis, then the background values computed using the MSK information will differ from the ones computed by the EAW bar graph.
Customers using GCOS v1.2 will be impacted when any of the following conditions are met:
- Generating Comparison Analysis results using probe masking
- Generating comparison analysis results using a baseline CHP file with probe masking
- Exporting CHP files generated in GCOS 1.2 which used probe masking
- Viewing CHP files in the EAW which used probe masking and generated in GCOS 1.2.
Other versions of GCOS and Comparison Analysis without probe masks are not affected.
Note: Mask files used for Normalization or Scaling are not affected by this issue. This issue is specific to Comparison Analysis with Mask Files.
- Download and install the GCOS v1.2.1 update
- Download the CHP Diagnostic Tool zip file
- Extract the files in the CHP Diagnostic Tool zip file and follow the included instructions. The CHP Diagnostic Tool will identify any affected CHP data and produce a text file of the results which can then be imported into GCOS Batch Analysis for batch correction of the affected data
- Contact your local Field Application Specialist (FAS) or local Affymetrix office if you have further questions
- GCOS v1.2.1 update only needs to be applied to GCOS v1.2 systems
- Point the web browser to the download link below, select and start the download
- The download file will be a zip (WinZip) file
- Open the zip file
- Extract the file (.exe file)
- Double click on the .exe file to launch the install program
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