Question: Tools to analyze Illumina's HumanHT-12 v4 microarray expression data?
gravatar for epigene
4.2 years ago by
United States
epigene490 wrote:

I got some gene expression data based on Illumina's HumanHT-12 v4 Expression microarray kit. The goal is to find differentially expressed genes. Does anyone have recommendations on tools to use to analyze the data? Could be a standalone package or R package or anything decent.


microarray gene expression • 2.2k views
ADD COMMENTlink written 4.2 years ago by epigene490

Do you have idat files ? Maybe look at this script.

ADD REPLYlink written 4.2 years ago by poisonAlien2.8k

Hi poisonAlien,

Thanks for sharing the AnalyzeBead script. The script ran with my data, however, my FDR return as 0.96 or higher which indicates there gatta be something wrong. Any suggestion?

ADD REPLYlink written 4.2 years ago by ElfC0

Hi, its hard to say without knowing anything about the data. Do you have replicates ?

ADD REPLYlink written 4.2 years ago by poisonAlien2.8k

Dear poisonAlien, I have downloaded GEO dataset based on Illumina HumanHT-12 V4.0 expression beadchip platform, the raw data contains 20 .adat files and 2 .txt files, I like to used your script for that purpose would you like to tell me where to edit this script and add my all .adat files to analyze. The RAW file is in tar format should I need to unzip. Kindly elaborate me from your precious time as I just start learning R and previously work on .cel files as .adat files are new for me and I want to learn it.

Thankyou in advance.

ADD REPLYlink written 2.8 years ago by flavia0
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