Closed: Microarray analysis of .idat files to identify degs
2
0
Entering edit mode
nia ▴ 30
@nia-12707
Last seen 4.8 years ago

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.

idat microarray • 377 views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 1026 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6