Dear fellows,
I want to work on a dataset and its based on platform "GPL10558" :Illumina HumanHT-12 V4.0 expression beadchip. After gunzipping the raw file I got 20 (.idat) files and 2 (.txt) files. I search this on bioconductor and biostar but I can't found the answer of my interest.
Objective: I want to identify DEGs after normalizing the RAW data as I am a student I would really appreciate if any one can provide me a R code to solve this query previously I work on matrix data on which I just use geoquery and limma function and identify DEGs but this time I want to normalize the RAW data and then I want to identify DEGs, mostly the code for normalization is available for .cel files. I am working on this query from december and its been a great learning experience but still my query is not solved.
*What I have tried: I simply download RAW file unzip it and apply this code on the same directory where my unzip idat files are present "https://raw.githubusercontent.com/PoisonAlien/beadAnalyze/master/analyzeBead.R" but it gives me no error and no result.*
Please tell me some easy to use code which can simply normalize the idat files and then do DEGs identification.
I would really grateful if my query will be solved by this platform.
Thankyou in advance.