Question: converting Affymetrix SNP 'intensity' data to LRR/BAF data
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gravatar for nikman.nor-hashim12
2.4 years ago by
nikman.nor-hashim120 wrote:

Hi all,

I am working on a big dataset that used Affymetrix platform for SNP genotyping. I have never worked on Affymetrix-related genotyping datasets. What I want to do is to identify copy number variations in chromosome 10 for n=120,000.

Let say I have a SNP 'intensity' data (chromosome 10) from Affymetrix platform, as shown below:

Person  Sex SNP1_A  SNP1_B  SNP2_A  SNP2B   ……… SNP30385_A  SNP30385_B

Person1 F   505.87  2824.05     305.99  810.14      2322.44     380.69

Person2 M   578.64  2541.85     218.58  968.26      375.97  2329.70

Person3 F   663.55  1539.48     4498.34     968.96      1334.80     1726.83

.

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.

Person120000

One way to convert Affy's intensity data into LRR/BAF data is by using PennCNV software. I have read the Penncnv-Affy guidelines for Axiom Arrays, but I could not identify which step that I have to start from…

http://penncnv.openbioinformatics.org/en/latest/user-guide/affy/
-Substep 1.4 LRR and BAF calculation: I suspect I have to start from this point to obtain the LRR/BAF data. However when I tried to use the script normalize_affy_geno_cluster.pl and load the above raw ‘intensity’ data, the input file was not the right one to be used by that script.

Therefore, can someone suggest a more direct way to obtain the LRR/BAF data from Affy's intensity data? If Penncnv-Affy workflow is the best one to use, what sort of files do I need to have to make it run? Any help will be very much appreciated! And I am sorry if all this is confusing to read.. Thank you.

Best wishes, Nikman

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