Many thanks to Wei for providing the information.

Vasu: Within GenePattern (
http://genepattern.broadinstitute.org/gp/pages/login.jsf), use the module
called "IlluminaExpressionFileCreator" (help file's available here:
http://tinyurl.com/43n42et). This creates GCT files from a set of Illumina
expression IDAT files. The .gct files can then be used for any downstream
analysis.

However, I am not sure how to do something similar in R to make use of the
.dat files.
Any comments welcome.

Thank you.

Cheers,
Chintanu

==================================================

On Fri, Oct 21, 2011 at 5:59 PM, vasu punj <punjv@yahoo.com> wrote:

>  Chintanu,
>
> Would you specify the link with in Gene pattern which will use .idat files
> please.
> Thanks.
>
> Vasu
>
>  *From:* Chintanu <chintanu@gmail.com>
> *To:* Wei Shi <shi@wehi.edu.au>
> *Cc:* bioc <Bioconductor@stat.math.ethz.ch>
> *Sent:* Thursday, October 20, 2011 10:35 PM
>
> *Subject:* Re: [BioC] Illumina array analysis
>
> Hello Wei,
>
> I have inherited these .idat files, and there seems to be no way that I can
> get the text file(s) that you have mentioned. And, you say that I can no
> way
> make any use of these files using r, and is not a good news for me.
>
> However, I know that tools like GenePattern (
> http://www.broadinstitute.org/cancer/software/genepattern/) uses .idat
> files; but I'm not sure whether similar to whatever process(es) being
> implemented at the backend of such tools can be deployed in r too !!
> Thank you.
>
> Cheers,
> Chintanu
>
> ========================================================================
> On Wed, Oct 19, 2011 at 11:55 AM, Wei Shi <shi@wehi.edu.au> wrote:
>
> > Chintanu,
> >
> > The .idat files are only useful if you want to perform a bead-level
> > analysis (each probe contains around ~15-30 beads). But having .idat
> files
> > does not mean you have the complete bead-level data. You will have to
> have
> > .txt files in your data as well,  which give the intensities for each
> bead.
> > But if the default setting of GenomeStudio/BeadStudio was used when your
> > bead chips were scanned, these .txt file will NOT be outputted. This
> means
> > you can not perform a bead-level analysis even you have these .idat
> files.
> >
> > In most of the microarray experiments using Illumina bead chips, only
> > probe-level data are available. Limma starts the Illumina data analysis
> from
> > reading in the probe level data (read.ilmn function), performs neqc
> > normalization and then carry out differential expression analysis using
> > eBayes moderated t statistics (this step is the same for all different
> > microarray platforms).
> >
> > Hope this helps.
> >
> > Cheers,
> > Wei
> >
> >  On Oct 19, 2011, at 11:41 AM, Chintanu wrote:
> >
> >  Hi,
> >
> > Thanks to John, Wei, and Miles Pufall.
> >
> > While looking at your recommended documents/vignettes, I can't seem to
> find
> > any way of reading in the .idat files. In case of Affymetrix, the .cel
> files
> > can be easily read in using functions like ReadAffy() from Affy package.
> For
> > spotted-arrays too, the .gpr files can be read easily.
> >
> > I have these .idat files that I'm hoping to analyse, but am unsure
> > regarding how I can read in the files, and (at the same time) can make
> use
> > of those recommended documents/vignettes.
> >
> > regards,
> > Chintanu
> >
> > =============================================================
> >
> >
> >>  > 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@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}}
> >> >
> >> > _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor@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 intended solely for
> >> the addressee.
> >> You must not disclose, forward, print or use it without the permission
> of
> >> the sender.
> >> ______________________________________________________________________
> >>
> >
> >
> >
> > ______________________________________________________________________
> > The information in this email is confidential and inte...{{dropped:10}}
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>

	[[alternative HTML version deleted]]

