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Looking For Snp'S That Are Significantly Differentially Expressed

I have SNP genotyping data from Illumina Bead xpress. I used Genome studio to generate reportfile. I am interested in doing some downstream analysis including looking for SNP's that are significantly differentially expressed in my contro group samples and diseased samples. Any suggestion is greatly appreciated and thanks in advance.

snps expression
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updated by Josh Herr Josh Herr • written by vigprasud vigprasud

SNP array and differential expression? You sound confused. Do you mean to say that you want to calculate whether SNPs are significantly more prevalent in either the disease or control group (i.e., you're doing an association study)?

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written by Devon Ryan Devon Ryan

Yes. I am sorry about the question not being very clear. I am trying to do association study and wanted to see if the SNP's are prevelent in Diseased or the normal group. Could you help me with any package that can be used for downstream analysis ..

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written by vigprasud vigprasud

There aren't any particular packages needed. You have, in effect, a 2x2 contigency table for each of your SNPs of interest. So, you could just use a Fisher's test, which is the fisher.test() function in R.

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written by Devon Ryan Devon Ryan

You are confused. Transcripts are differentially expressed, not SNPs. Suggest you take some time to figure out what you are trying to do.

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written by Neilfws Neilfws

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