Hi all, Since I am very naive to GWAS analysis using Illumina SNP-array platform, I am not able to find raw files equivalents to .CEL files from Affymetrix in GEO for Illumina. Whatever files are present in GEO repositories are not readable with crlmm package of R/bioconductor. Is there any way to get data from GEO of Illumina SNP-array platform and proceed data analysis with R/bioconductor packages? I want to read this data in plink further. Please guide me for feasibility. Below is the data structure present in GEO:
Name 5995908004_R01C01.X Raw 5995908004_R01C01.X 5995908004_R01C01.YRaw 5995908004_R01C01.Y rs1000002 3816 0.2455007 3347 0.2471608 rs1000003 13070 0.9807821 7838 0.6620893 rs10000030 1160 0.0263103 4894 0.3981797 rs10000037 3208 0.1807805 8758 0.7633662 rs10000041 8445 0.6252059 1454 0.06045614
Regards, Mandar R. Bobade.
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Could you tell the GSE id of the dataset you're looking into. The dataset on GEO that contains 5995908004_R01C01, (GSE43406) does include genotypes in the datatables, Furthermore the dataset seems to contain samples for testing the suitability of FFPE samples, which is not something you'd generally do a GWAS type of analysis on.
The GSE ID is 43406. I think you have found it correctly. Can you guide me in this aspect? i.e. how to go ahead with Illumina SNP-array data from GEO for GWAS analysis using R/bioconductor packages, at least till I get get SNP or genotyping calls which I can later convert into such a format which will be useful in plink. Any ideal data set to go ahead with?