R help - Apr 2012 - Read .idat Illumina files in R

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
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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.

Best,
Moiz


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]]
> 
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