Background Correction Method
Select a method for background correction. As availability of specific methods varies by process, you might see different combinations of the following choices.
The methods are summarized as follows:
|
Method |
Description |
|
None |
Applies no background correction. |
|
Kernel Surface |
Subtracts a smooth background surface computed by averaging over blocks of data. Shifted Log2 transformation is recommended when applying the Kernel Surface method. Adding a constant (16 to 32) as a Shifting Factor will help stabilize the variation at the low expression range after log transformation. |
|
MM |
Uses the mismatch values as background to be subtracted from perfect match values. Note: This method cannot be applied for WT-Gene and Exon arrays. |
|
RMA |
Applies RMA (Robust Multi-array Average) background correction. |
|
GCRMA |
Applies GCRMA (Gene Chip Robust Multi-array Average) background correction. Note: This method requires the corresponding tab-formatted probe sequence file. |
To Choose a Background Correction Method:
| 8 | Click the radio button corresponding to the desired method. |