Transcript Instrument Evolution

Short description on how to
use dChip SNP
Please watch in slide show mode
Updated 02-24-2004
dChip SNP
• Available upon request from Cheng Li
• Please send Email to:
•
•
•
•
– Cheng Li at: [email protected]
Parametric linkage analysis
– Dominant
– Recessive
Genome annotation with Genes,
Cytoband, Lod score and SNP information
in one window
No error correction neede
Runs up to 17 bites
Step-by-Step
• Export GDAS files
– Only the Affy SNPID and Genotypes need to
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be included
Generate the standard pedigree file as
discussed
Add an array column in the pedigree file
before the affection status
This column needs to have the identical name
as the experiment name in GDAS
For individuals without genotypes add “Nofile”
in the field
Save as text file (tab delimited)
dChip SNP : Data file
dChip SNP : Pedigree file
dChip SNP: Import data
dChip SNP: Import data
1. Assign a name
for the analysis
2. Select the data
file
3. Select SNP
analysis
4. Press
OK
dChip SNP: Import data
dChip SNP: Import annotation files
(all files are distributed with the software)
1. Select
2. Select
3. Select
4. Select
(optional)
5. Select
Genotype
Information
dChip SNP: Linkage analysis
Select the
pedigree file
Define:
Disease allele freq.
Penetrance
Disease model
Simulation?
Press: OK
LOD Graph