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]]
> >>
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> >
> >
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