Microarray analysis of illumina microchips

Question

[Adnaane]

Hi all,

It's been a while since I started working on microarray analysis. I worked on the affymetrix chips.

My current project requires microarrays analysis or processing of data generated from "Illumina HumanHT-12 V4.0 expression beadchip". I made some researches and also read limma user's guide, I dont even know how i should start because when i download the RAW file it contains another two compressed samples. So let me know please or give me some tips about what should I do to get a ready-to-use files from that type of raw data (eg. of reference = GSE54293, gathered from GEO) for further data processing and analysis.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54293

I took a look at the user's guide of limma, some documents and google but it's not very helpful for me. Thanks for your help in advance, and I will appreciate if you could give me the exact code.

Answer 1

[Kevin Blighe]

For whatever reason, the way in which Illumina array data is uploaded onto GEO is not readily conducive to analysis by the pipelines (including Limma's) that have been developed for these arrays. So, customised analyses are needed.

In cases like this (your case), I encourage users to use the GEO2R functionality in order to obtain the data directly from GEO:

library(Biobase)
library(GEOquery)

# load series and platform data from GEO
gset <- getGEO("GSE54293", GSEMatrix =TRUE, getGPL=FALSE)
if (length(gset) > 1) idx <- grep("GPL10558", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

If, instead, you want to process the data yourself, you just need the GSE54293_Non_normalized_data.txt.gz file, and you can follow my general guidance here: A: illumina Arrays Illumina HumanHT-12 V3.0 expression beadchip reading data

Kevin

[Adnaane]

Thank you for your help Kevin. I have another question about the link you add in your answer. I wanted to use its method for my case but i got a problem : i didn't find any BGX file in my example.

[Kevin Blighe]

Oh yes, I think that the BGX file is in the other file, GSE54293_RAW.tar (well, there are 2 files contained in this TAR file - you can try both). Note that the BGX format is merely a compressed tab-delimited file - it's no special format.

[Adnaane]

Thanks a lot Kevin ! I appreciate it.