Question: Illumina SNP microarray process
0
gravatar for hntiger1688
5.3 years ago by
hntiger168830
United States
hntiger168830 wrote:

Hi, everyone.

Previously, I was major in RNA microarray analysis. 

However, It is my first time to analysis the SNP microarray data.

I downloaded the SNP microarray from GEO the GEO accession ID is GSE43406.

The SNP microarray platform is Illumina Human1Mv1 DNA Analysis BeadChip

I want to get the RSID and genotype of each SNP.

I would be really appreciate to anyone who give me help!

Thanks!

snp R • 2.0k views
ADD COMMENTlink modified 5.2 years ago by Sam2.5k • written 5.3 years ago by hntiger168830
0
gravatar for Sam
5.2 years ago by
Sam2.5k
New York
Sam2.5k wrote:

I am not sure if it is the same, but this is the code I use for expression microarray to extract the ids:

 

gpl=getGEO("GPL1261", destdir=".") //Select the appropriate platform here and replace the GPL1261
id2Name=Table(gpl)[,c(1,11)] //You will want to colnames(Table(gpl)) to get the RSID, I think mine is for the gene name

 

ADD COMMENTlink written 5.2 years ago by Sam2.5k

Thanks for your help!

Yeah, I have tried this but I takes long time to get the Data.

2014-11-05 17:07 GMT+08:00 Sam on Biostar <notifications@biostars.org>:

ADD REPLYlink written 5.2 years ago by hntiger168830
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