Question: how to use idat file for analyses in bioconductor
0
gravatar for Kritika
4.3 years ago by
Kritika260
India
Kritika260 wrote:

Hello all,

I want to know how to use idat file for analysis in bioconductor.

I read certain packages manual (limma and lumi). There it is said for analyses i need .txt file which is generated from genome studio.

For my dummy sample i run the genome studio too. How i will get text files for analyses using lumi or limma

I also tried using illuminaio which only read idat

Is there any procedure in bioconductor which will convert idat to txt. Or it is obtained from genomestudio? if yes then how to get it from genome studio?

Also one more question is there any script which directly read idat file ? i tried one script which is giving me error.

please help

Thank You

 

microarray idatfile illumina • 1.7k views
ADD COMMENTlink modified 4 months ago by freeseek50 • written 4.3 years ago by Kritika260
1
gravatar for Gordon Smyth
5 months ago by
Gordon Smyth1.6k
Australia
Gordon Smyth1.6k wrote:

The read.idat function in the limma package will read the idat files directly into an expression object.

ADD COMMENTlink written 5 months ago by Gordon Smyth1.6k
0
gravatar for freeseek
4 months ago by
freeseek50
freeseek50 wrote:

You can also use my bcftools plugin gtc2vcf with option --idat to see the content of an IDAT file in text format

ADD COMMENTlink written 4 months ago by freeseek50
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