I'm working with public dataset from here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67047. I have downloaded the Series Matrix file, and I can extract metadata and genotype from it. I have some questions as follow: How can I convert Affymetrix A/B Allele to Ref/Alt format? I have read this post, but it doesn't seem to be right, according to Affymetrix document. I think I can download dbsnp data, and do cross query between affymatrix array and dbsnp, but it is really time-consuming. Is there any package or tool for this task? How can I preprocess the missing call? I can fill them with the mode of the SNP, but some papers try to fill them by HWE or other methods, if someone can show me how to process the data would be really great! Thank you very much.

Preprocessing Affymetrix SNP Array Matrix

Bioinformatics Asked by Thanh Nguyen on November 17, 2020

I’m working with public dataset from here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67047. I have downloaded the Series Matrix file, and I can extract metadata and genotype from it. I have some questions as follow:

How can I convert Affymetrix A/B Allele to Ref/Alt format? I have read this post, but it doesn’t seem to be right, according to Affymetrix document. I think I can download dbsnp data, and do cross query between affymatrix array and dbsnp, but it is really time-consuming. Is there any package or tool for this task?
How can I preprocess the missing call? I can fill them with the mode of the SNP, but some papers try to fill them by HWE or other methods, if someone can show me how to process the data would be really great!

Thank you very much.

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