[BioC] Illumina array analysis

Belmont, John W jbelmont at bcm.edu
Tue Oct 18 14:33:26 CEST 2011


Consider using the lumi package for normalization and data QC. Lumi implements the variance stabilization and robust spline normalization procedure that takes advantage of the multiple bead data produced by Illumina arrays.

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Wei Shi
Sent: Monday, October 17, 2011 9:11 PM
To: Chintanu
Cc: bioc
Subject: Re: [BioC] Illumina array analysis

Hi Chintanu,

There is a case study for analyzing Illumina BeadChip data in limma user's guide. Type the following command in your R to bring up limma user's guide and then have a look at section 11.7.

limmaUsersGuide()


Cheers,
Wei

On Oct 18, 2011, at 12:55 PM, Chintanu wrote:

> Hi,
> 
> I'm new to my exploration with analysing illumina microarray data using r.
> While looking for some example case study (so that I can do my analysis
> taking pointers from that/those examples), I am unable to find anything
> useful. I would appreciate if you could either provide me with some pointers
> in that direction or share your codes that you have done while doing your
> illumina analysis.
> 
> I am mainly interested in the following: (i) read in the illumina files &
> check the quality of the files, (iii) normalization (any type), (iii)
> applying Limma and pick the differentially expressed genes.
> 
> Thank you.
> 
> regards,
> Chintanu
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


______________________________________________________________________
The information in this email is confidential and intend...{{dropped:9}}



More information about the Bioconductor mailing list