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.
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?