[BioC] Read .idat Illumina files in R

Moiz Bootwalla msbootwalla at gmail.com
Wed Apr 11 16:14:20 CEST 2012

Hi Ekta,

You can use the bioconductor package methylumi to read in .idat files. The function methylumIDAT() will read in .idat files and provide you with beta values along with the M and U values as a MethyLumiSet object. You can then use the functions methylumi.bgcorr() and normalizeMethyLumiSet() to background correct and normalize your data. See the vignette for more details.


On Apr 11, 2012, at 1:46 AM, Ekta Jain wrote:

> Dear Bioc and R List Users,
> I am having trouble analysing illumine data generated from BeadScan. I have .idat files and JPEG images. I realise that i need bead-level summary data to be able to begin quality control followed by normalization. Is there a way i can read .idat files for expression analysis or do i need to go back to BeadScan and generate .txt files/tiff files ?
> Appreciate any help here.
> Many Thanks,
> Ekta Jain
> The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a!
> nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email.
> www.jubl.com
> 	[[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

More information about the Bioconductor mailing list