I am trying to find a package that can handle the iscan SNP genotyping data. I looked at Bioconductor 2.8 and found the following somewhat related just by name, and surfing the details, but I could not get categorically saying that they can handle iscan data.
beadarray
Quality assessment and low-level analysis for Illumina BeadArray data
beadarraySNP
Normalization and reporting of Illumina SNP bead arrays
BeadDataPackR
Compression of Illumina BeadArray data
SNPchip
Classes and Methods for high throughput SNP chip data
snpMatrix
The snp.matrix and X.snp.matrix classes
snpStats
SnpMatrix and XSnpMatrix classes and methods
Please share your understanding or experience on suitable package I can use to process the iscan ( http://www.illumina.com/systems/iscan.ilmn) data from the step 0.
Thanks;
The beadarray package now contains a function called processSwathData(), which should transform this data into a format beadarray can handle.
Do you have one text file per sample? Or just the .tif images? You will need files such as _perBeadfile.txt to use this. I am unsure if you can read bead-level data from the .tif files and the .loc files only.
Have you looked into the crlmm package at all? That is capable of reading Illumina 'idat' files and performing normalization and genotyping.
I am one of the developers of beadarray and as mentioned above we recently made some changes to allowg iScan data to be read in. Please feel free to give it a go and get in touch if you have any problems. We'd be happy to look at a small sample of the data if that would help.
The beadarray package was mainly developed with expression arrays in mind (as these are the data we usually have to deal with in-house). However it should be perfectly possible to perform quality assessment and low-level analysis in the same manner regardless of the assay type. One big complication of SNP data is dealing with how to summarize the two channels into sensible quantities for analysis, but beadarray hopefully provides enough flexibility to allow this.
