Newport iServer MicroServer iTHX-M, Operator'S Manual, Page: 138 / 414

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Affymetrix GeneChip
®
Genotyping Analysis Software User’s Guide
The parameters for that array type are displayed.
B.
Click the item you want to change.
The current value for the item is displayed (Figure 4.17) .
C.
Enter a new value for the item.
3.
To return all settings to the factory set defaults, click Default .
4.
Click OK .
The new values are entered in the algorithm.
The algorithm settings are described in MPAM Mapping Algorithm
Settings, on page 331 .
Using the Gender Attribute Values
If you know the gender for a sample, you can assign a gender attribute
value to it when performing the experiment with GeneChip
Operating Software (GCOS). You can then define these gender
attribute values in GTYPE, so GTYPE can use the appropriate male
or female model for the sex chromosomes. If the gender attribute is not
set or not found in the sample’s template, the MPAM mapping gender
determination algorithm is used to determine the gender.
For more information, see Determining Sample Gender, on page 328 .
Changing the settings may change the call rate and accuracy of
genotypes.
The accuracy of the gender determining algorithm depends upon
the SNP call rate for the sample. Samples with lower call rates may
have inaccurate gender calls, which will then affect the accuracy of
allele calls for SNPs on the X chromosome. You should assign a
gender attribute value to the sample whenever possible.
GTYPE_manual.book Page 130 Wednesday, August 2, 2006 11:31 AM