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]]
> >>
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